# ==============================================================================
# Functions for defining MAPPINGS between table column values and visual
# properties, organized into sections:
#
# I. General functions for creating and applying mappings for node, edge and
# network properties
# II. Specific functions for defining particular node, edge and network
# properties
# III. Functions for generating and mapping property values to colors,
# opacities, sizes, heights, widths and shapes
#
# ==============================================================================
# I. General Functions
# ------------------------------------------------------------------------------
#' Creates a mapping between an attribute and a visual property
#'
#' @description Generates the appropriate data structure for the "mapping" parameter
#' in updateStyleMapping.
#' @details The paired list of values must be of the same length or mapping will fail.
#' For gradient mapping, you may include two additional visual.prop.values in the
#' first and last positions to map respectively to values less than and greater
#' than those specified in table.column.values. Mapping will also fail if the
#' data type of table.column.values does not match that of the existing table.column.
#' Note that all imported numeric data are stored as Integers or Doubles in
#' Cytosacpe tables; and character or mixed data are stored as Strings.
#' @param visual.prop (char) name of visual property to map
#' @param table.column (char) name of table column to map
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p)
#' @param table.column.values (list) list of values paired with visual.prop.values; skip for passthrough mapping
#' @param visual.prop.values (list) list of values paired with table.column.values; skip for passthrough mapping
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return (network=network, base.url=base.url) ready to convert into JSON by style mapping operations
#' @seealso updateStyleMapping getVisualPropertyNames
#' @examples
#' \donttest{
#' mapVisualProperty('node fill color','score','c',c(-4.0,0.0,9.0),c('#99CCFF','#FFFFFF','#FF7777'))
#' mapVisualProperty('node shape','type','d',c('protein','metabolite'),c('ellipse','rectangle'))
#' mapVisualProperty('node label','alias','p')
#' }
#' @section List of visual properties:
#' \tabular{lll}{
#' Node Border Stroke \tab Edge Bend \tab Network Background Paint \cr
#' Node Border Paint \tab Edge Curved \tab Network Center X Location \cr
#' Node Border Transparency \tab Edge Label \tab Network Center Y Location \cr
#' Node Border Width \tab Edge Label Color \tab Network Center Z Location \cr
#' Node CustomGraphics 1-9 \tab Edge Label Font Face \tab Network Depth \cr
#' Node CustomGraphics Position 1-9 \tab Edge Label Font Size \tab Network Edge Selection \cr
#' Node CustomGraphics Size 1-9 \tab Edge Label Transparency \tab Network Height \cr
#' Node CustomPaint 1-9 \tab Edge Label Width \tab Network Node Selection \cr
#' Node Depth \tab Edge Line Type \tab Network Scale Factor \cr
#' Node Fill Color \tab Edge Paint \tab Network Size \cr
#' Node Height \tab Edge Selected \tab Network Title \cr
#' Node Label \tab Edge Selected Paint \tab Network Width \cr
#' Node Label Color \tab Edge Source Arrow Selected Paint \tab \cr
#' Node Label Font Face \tab Edge Source Arrow Shape \tab \cr
#' Node Label Font Size \tab Edge Source Arrow Size \tab \cr
#' Node Label Position \tab Edge Source Arrow Unselected Paint \tab \cr
#' Node Label Transparency \tab Edge Stroke Selected Paint \tab \cr
#' Node Label Width \tab Edge Stroke Unselected Paint \tab \cr
#' Node Network Image Visible \tab Edge Target Arrow Selected Paint \tab \cr
#' Node Paint \tab Edge Target Arrow Shape \tab \cr
#' Node Selected \tab Edge Target Arrow Size \tab \cr
#' Node Selected Paint \tab Edge Target Arrow Unselected Paint \tab \cr
#' Node Shape \tab Edge Tooltip \tab \cr
#' Node Size \tab Edge Transparency \tab \cr
#' Node Tooltip \tab Edge Unselected Paint \tab \cr
#' Node Transparency \tab Edge Visible \tab \cr
#' Node Visible \tab Edge Visual Property \tab \cr
#' Node Width \tab Edge Width \tab \cr
#' Node X Location \tab \tab \cr
#' Node Y Location \tab \tab \cr
#' Node Z Location \tab \tab \cr
#' }
#' @export
mapVisualProperty <- function(visual.prop, table.column, mapping.type, table.column.values,
visual.prop.values, network=NULL, base.url=.defaultBaseUrl){
suid <- getNetworkSuid(network,base.url)
#process mapping type
mapping.type.name = switch(mapping.type, 'c'='continuous','d'='discrete','p'='passthrough',mapping.type)
#processs visual property, including common alternatives for vp names :)
visual.prop.name = toupper(gsub("\\s+","_",visual.prop))
visual.prop.name = switch(visual.prop.name,
'EDGE_COLOR'='EDGE_UNSELECTED_PAINT',
'EDGE_THICKNESS'='EDGE_WIDTH',
'NODE_BORDER_COLOR'='NODE_BORDER_PAINT',
'NODE_BORDER_LINE_TYPE'='NODE_BORDER_STROKE',
visual.prop.name)
#check visual prop name
if(!visual.prop.name %in% getVisualPropertyNames(base.url = base.url)){
stop(paste0('Could not find ',visual.prop.name,
'. Run getVisualPropertyNames() to retrieve property names.'))
}
#check mapping column and get type
tp = tolower(strsplit(visual.prop.name,"_")[[1]][1])
table = paste0('default',tp)
res <- cyrestGET(paste('networks',suid,'tables',table,'columns',sep='/'),base.url=base.url)
table.column.type = NULL
for(i in seq_len(length(res))){
if(res[[i]]$name==table.column){
table.column.type = res[[i]]$type
break
}
}
if(is.null(table.column.type))
stop(paste0('Could not find ',table.column,' column in ',table,' table.'))
#construct visual property map
visual.prop.map <- list(
mappingType=mapping.type.name,
mappingColumn=table.column,
mappingColumnType=table.column.type,
visualProperty=visual.prop.name
)
if(mapping.type.name=='discrete'){
map <- list()
for (i in seq_len(length(table.column.values))) {
map[[i]] <- list(key=toString(table.column.values[i]), value=toString(visual.prop.values[i]))
}
visual.prop.map$map=map
}else if(mapping.type.name=='continuous'){
points <- list()
#check for extra lesser and greater values
propValCount <- length(visual.prop.values)
colValCount <- length(table.column.values)
if (propValCount-colValCount == 2){
for (i in seq_len(colValCount)) {
points[[i]] <- list(value=table.column.values[i],
lesser=visual.prop.values[i+1],
equal=visual.prop.values[i+1],
greater=visual.prop.values[i+1]) #note offset
}
#then correct extreme values
points[[1]] <- list(value=table.column.values[1],
lesser=visual.prop.values[1],
equal=visual.prop.values[2],
greater=visual.prop.values[2])
points[[colValCount]] <- list(value=table.column.values[colValCount],
lesser=visual.prop.values[colValCount+1],
equal=visual.prop.values[colValCount+1],
greater=visual.prop.values[colValCount+2])
}
else if (propValCount-colValCount == 0) {
for (i in seq_len(colValCount)) {
points[[i]] <- list(value=table.column.values[i],
lesser=visual.prop.values[i],
equal=visual.prop.values[i],
greater=visual.prop.values[i])
}
}
else {
stop ("Table.column.values and visual.prop.values don't match up.")
}
visual.prop.map$points=points
}
return(visual.prop.map)
}
# ------------------------------------------------------------------------------
#' Updates a visual property mapping in a style
#'
#' @description Updates the visual property mapping, overriding any prior mapping. Creates a
#' visual property mapping if it doesn't already exist in the style.
#' @details Requires visual property mappings to be previously created, see mapVisualProperty.
#' @param style.name (char) name for style
#' @param mapping a single visual property mapping, see mapVisualProperty
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return server response
#' @export
#' @seealso mapVisualProperty
#' @examples
#' \donttest{
#' updateStyleMapping('myStyle',mapVisualProperty('node label','name','p'))
#' }
updateStyleMapping <- function(style.name, mapping, base.url=.defaultBaseUrl){
visual.prop.name = mapping$visualProperty
# set default style
if(is.null(style.name)){
style.name <- 'default'
message('style.name not specified, so updating "default" style.')
}
# check if vp exists already
res <- cyrestGET(paste('styles', style.name,'mappings',sep = '/')
,base.url=base.url)
vp.list <- lapply(res, function(x) unname(x['visualProperty'][[1]]))
if(visual.prop.name %in% vp.list){
exists = TRUE
} else {
exists = FALSE
}
if(exists==TRUE){
res <- invisible(cyrestPUT(paste('styles', style.name,'mappings',visual.prop.name, sep = '/'),
body=list(mapping),
base.url=base.url))
}
else {
res <- invisible(cyrestPOST(paste('styles', style.name,'mappings',sep = '/'),
body=list(mapping),
base.url=base.url))
}
Sys.sleep(get(".MODEL_PROPAGATION_SECS", envir=RCy3env)) ## NOTE: TEMPORARY SLEEP "FIX"
return(res)
}
# ------------------------------------------------------------------------------
#' @title Delete Style Mapping
#'
#' @description Deletes a specified visual style mapping from specified style.
#' @param style.name (char) name for style
#' @param visual.prop (char) name of visual property to map.
#' See getVisualPropertyNames().
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' deleteStyleMapping()
#' }
#' @export
deleteStyleMapping<-function(style.name, visual.prop, base.url=.defaultBaseUrl){
# check if vp exists already
res <- cyrestGET(paste('styles', style.name,'mappings',sep = '/')
,base.url=base.url)
vp.list <- lapply(res, function(x) unname(x['visualProperty'][[1]]))
if(visual.prop %in% vp.list){
exists = TRUE
} else {
exists = FALSE
}
if(exists==TRUE){
invisible(cyrestDELETE(paste('styles', style.name,'mappings',visual.prop, sep = '/'),
base.url=base.url))
}
}
# ------------------------------------------------------------------------------
#' @title Get Style Mapping
#'
#' @description Retrieve the values the define the mappings for a given
#' visual property in a style.
#' @param visual.prop Name of the visual property, e.g., NODE_FILL_COLOR
#' @param style.name Name for style; default is the 'default' style
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return List of named values defining the visual property mappings
#' @examples \donttest{
#' getStyleMapping()
#' }
#' @seealso getVisualPropertyNames
#' @export
getStyleMapping <- function(visual.prop, style.name=NULL,
base.url=.defaultBaseUrl){
if(is.null(style.name)){
style.name <- 'default'
message('style.name not specified, so using "default" style.')
}
cyrestGET(paste('styles',style.name,'mappings', visual.prop, sep = '/'),
base.url=base.url)
}
# ------------------------------------------------------------------------------
#' @title Get All Style Mappings
#'
#' @description Retrieve the values the define all the mappings per visual
#' property in a given style.
#' @param style.name Name for style; default is the 'default' style
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return List of lists with named values defining the visual property mappings
#' @examples \donttest{
#' getStyleMapping()
#' }
#' @export
getAllStyleMappings <- function(style.name=NULL,
base.url=.defaultBaseUrl){
if(is.null(style.name)){
style.name <- 'default'
message('style.name not specified, so using "default" style.')
}
cyrestGET(paste('styles',style.name,'mappings', sep = '/'),
base.url=base.url)
}
# ==============================================================================
# II. Specific Functions
# ==============================================================================
# II.a. Node Properties
# Pattern: (1) prepare mapVisualProperty, (2) call updateStyleMapping()
# ------------------------------------------------------------------------------
#' @title Set Node Border Color Mapping
#'
#' @description Map table column values to colors to set the node border color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeBorderColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setNodeBorderColorMapping('score', colors=paletteColorBrewerRdBu)
#' setNodeBorderColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setNodeBorderColorMapping <- function (table.column, table.column.values=NULL, colors=NULL,
mapping.type='c', default.color=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check for color palette use case
if(typeof(colors) == "closure"){ #i.e., name of palette function
if(is.null(table.column.values)){
auto.map<-.genColorMap('node',table.column,colors,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
colors<-auto.map$colors
} else {
colors <- colors(length(table.column.values))
}
}
# check if colors are formatted correctly
for (color in colors){
.checkHexColor(color)
}
# set default color
if(!is.null(default.color))
setNodeBorderColorDefault(default.color, style.name, base.url=base.url)
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_BORDER_PAINT",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_BORDER_PAINT",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_BORDER_PAINT",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Border Opacity Mapping
#'
#' @description Sets opacity for node border only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeBorderOpacityMapping('score')
#' setNodeBorderOpacityMapping('score', opacities=c(0,100))
#' setNodeBorderOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeBorderOpacityMapping <- function(table.column, table.column.values=NULL,
opacities=NULL, mapping.type='c',
default.opacity=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'node',network, base.url))
stop("Table column does not exist. Please try again.")
for (o in opacities){
.checkOpacity(o)
}
if(!is.null(default.opacity)){
.checkOpacity(default.opacity)
setVisualPropertyDefault(
list(visualProperty = "NODE_BORDER_TRANSPARENCY", value = default.opacity),
style.name, base.url)
}
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
opacities<-auto.map$opacities
}
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp1 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp1 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp1 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("Mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Border Width Mapping
#'
#' @description Map table column values to widths to set the node border width.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param widths List of width values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.width Width value to set as default for all unmapped values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeBorderWidthMapping('score')
#' setNodeBorderWidthMapping('score', widths=c(1,10))
#' setNodeBorderWidthMapping('score', c(0,30), c(1,5))
#' }
#' @export
setNodeBorderWidthMapping <- function (table.column, table.column.values=NULL, widths=NULL,
mapping.type='c', default.width=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.width))
setNodeBorderWidthDefault(default.width, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genDimMap('node',table.column,widths,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
widths<-auto.map$dims
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_BORDER_WIDTH",table.column, 'c',
table.column.values, widths,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_BORDER_WIDTH",table.column, 'd',
table.column.values, widths,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_BORDER_WIDTH",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Color Mapping
#'
#' @description Map table column values to colors to set the node fill color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeColorMapping('score', c(-5,0,5), c('#5577FF','#FFFFFF','#FF7755'))
#' setNodeColorMapping('score', colors=paletteColorBrewerRdBu)
#' setNodeColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setNodeColorMapping <- function (table.column, table.column.values=NULL, colors=NULL,
mapping.type='c', default.color=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check for color palette use case
if(typeof(colors) == "closure"){ #i.e., name of palette function
if(is.null(table.column.values)){
auto.map<-.genColorMap('node',table.column,colors,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
colors<-auto.map$colors
} else {
colors <- colors(length(table.column.values))
}
}
# check if colors are formatted correctly
for (color in colors){
.checkHexColor(color)
}
# set default
if(!is.null(default.color))
setNodeColorDefault(default.color, style.name, base.url=base.url)
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_FILL_COLOR",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_FILL_COLOR",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_FILL_COLOR",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Combo Opacity Mapping
#'
#' @description Sets opacity for node fill, border and label all together.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeComboOpacityMapping('score')
#' setNodeComboOpacityMapping('score', opacities=c(0,100))
#' setNodeComboOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeComboOpacityMapping <- function (table.column, table.column.values=NULL,
opacities=NULL, mapping.type='c',
default.opacity=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check if opacities are formatted correctly
for (o in opacities){
.checkOpacity(o)
}
# set default
if(!is.null(default.opacity)){
.checkOpacity(default.opacity)
setVisualPropertyDefault(
list(visualProperty = "NODE_TRANSPARENCY", value = default.opacity),
style.name, base.url)
setVisualPropertyDefault(
list(visualProperty = "NODE_BORDER_TRANSPARENCY", value = default.opacity),
style.name, base.url)
setVisualPropertyDefault(
list(visualProperty = "NODE_LABEL_TRANSPARENCY", value = default.opacity),
style.name, base.url)
}
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
opacities<-auto.map$opacities
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
mvp2 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
mvp3 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
mvp2 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
mvp3 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
mvp2 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
mvp3 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp1, base.url = base.url)
updateStyleMapping(style.name, mvp2, base.url = base.url)
updateStyleMapping(style.name, mvp3, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Fill Opacity Mapping
#'
#' @description Sets opacity for node fill only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeFillOpacityMapping('score')
#' setNodeFillOpacityMapping('score', opacities=c(0,100))
#' setNodeFillOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeFillOpacityMapping <- function(table.column, table.column.values=NULL,
opacities=NULL, mapping.type='c',
default.opacity=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'node',network, base.url))
stop("Table column does not exist. Please try again.")
for (o in opacities){
.checkOpacity(o)
}
if(!is.null(default.opacity)){
.checkOpacity(default.opacity)
setVisualPropertyDefault(
list(visualProperty = "NODE_TRANSPARENCY", value = default.opacity),
style.name, base.url)
}
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
opacities<-auto.map$opacities
}
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Font Face Mapping
#'
#' @description Sets font face for node labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping
#' @param fonts List of string specifications of font face, style and size, e.g.,
#' c("SansSerif,plain,12", "Dialog,plain,10")
#' @param mapping.type (char) discrete or passthrough (d,p);
#' default is discrete
#' @param default.font String specification of font face, style and size, e.g.,
#' "SansSerif,plain,12" or "Dialog,plain,10"
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeFontFaceMapping("myfonts", c("normal","small"),
#' c("SansSerif,plain,12", "Dialog,plain,10"))
#' }
#' @export
setNodeFontFaceMapping <- function(table.column, table.column.values,
fonts, mapping.type='d',
default.font=NULL,
style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'node',network, base.url))
stop("Table column does not exist. Please try again.")
if(!is.null(default.font)){
setVisualPropertyDefault(
list(visualProperty = "NODE_LABEL_FONT_FACE", value = default.font),
style.name, base.url)
}
if (mapping.type %in% c('continuous','c','interpolate')) {
stop("Continuous mapping of font face values is not supported.")
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp1 <- mapVisualProperty("NODE_LABEL_FONT_FACE",table.column, 'd',
table.column.values, fonts,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp1 <- mapVisualProperty("NODE_LABEL_FONT_FACE",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Font Size Mapping
#'
#' @description Map table column values to sizes to set the node size.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param sizes List of sizes to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.size Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeFontSizeMapping('score')
#' setNodeFontSizeMapping('score', sizes=c(6,24))
#' setNodeFontSizeMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeFontSizeMapping <- function (table.column, table.column.values=NULL, sizes=NULL,
mapping.type='c', default.size=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.size))
setNodeFontSizeDefault(default.size, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genDimMap('node',table.column,sizes,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
sizes<-auto.map$dims
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_LABEL_FONT_SIZE",table.column, 'c',
table.column.values, sizes,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_LABEL_FONT_SIZE",table.column, 'd',
table.column.values, sizes,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_LABEL_FONT_SIZE",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Height Mapping
#'
#' @description Map table column values to the node heights.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param heights List of height values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.height Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @details Using this function will unlock node width and height to use
#' separate values.
#' @examples \donttest{
#' setNodeHeightMapping('score')
#' setNodeHeightMapping('score', heights=c(30,80))
#' setNodeHeightMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeHeightMapping <- function (table.column, table.column.values=NULL, heights=NULL,
mapping.type='c', default.height=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
lockNodeDimensions(FALSE, style.name,base.url)
# set default
if(!is.null(default.height))
setNodeHeightDefault(default.height, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genDimMap('node',table.column,heights,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
heights<-auto.map$dims
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_HEIGHT",table.column, 'c',
table.column.values, heights,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_HEIGHT",table.column, 'd',
table.column.values, heights,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_HEIGHT",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Label Mapping
#'
#' @description Pass the values from a table column to display as node labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeLabelMapping('name')
#' }
#' @export
setNodeLabelMapping <- function (table.column, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'node',network, base.url)) return()
mvp <- mapVisualProperty("NODE_LABEL", table.column, 'p',
network = network, base.url = base.url)
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Label Color Mapping
#'
#' @description Map table column values to colors to set the node border color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeLabelColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setNodeLabelColorMapping('score', colors=paletteColorBrewerRdBu)
#' setNodeLabelColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setNodeLabelColorMapping <- function (table.column, table.column.values=NULL, colors=NULL,
mapping.type='c', default.color=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check for color palette use case
if(typeof(colors) == "closure"){ #i.e., name of palette function
if(is.null(table.column.values)){
auto.map<-.genColorMap('node',table.column,colors,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
colors<-auto.map$colors
} else {
colors <- colors(length(table.column.values))
}
}
# check if colors are formatted correctly
for (color in colors){
.checkHexColor(color)
}
# set default
if(!is.null(default.color))
setNodeLabelColorDefault(default.color, style.name, base.url=base.url)
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_LABEL_COLOR",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_LABEL_COLOR",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_LABEL_COLOR",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Label Opacity Mapping
#'
#' @description Sets opacity for node label only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeLabelOpacityMapping('score')
#' setNodeLabelOpacityMapping('score', opacities=c(0,100))
#' setNodeLabelOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeLabelOpacityMapping <- function(table.column, table.column.values=NULL,
opacities=NULL, mapping.type='c',
default.opacity=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'node',network, base.url))
stop("Table column does not exist. Please try again.")
for (o in opacities){
.checkOpacity(o)
}
if(!is.null(default.opacity)){
.checkOpacity(default.opacity)
setVisualPropertyDefault(
list(visualProperty = "NODE_LABEL_TRANSPARENCY", value = default.opacity),
style.name, base.url)
}
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
opacities<-auto.map$opacities
}
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp1 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp1 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp1 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Shape Mapping
#'
#' @description Map table column values to shapes to set the node shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to
#' perform an automatic mapping to available shapes. See \link{getNodeShapes}
#' @param default.shape Shape to set as default. See \link{getNodeShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeShapeMapping('type')
#' setNodeShapeMapping('type',c('protein','dna'),c('ELLIPSE','RECTANGLE'))
#' }
#' @export
setNodeShapeMapping <- function (table.column, table.column.values=NULL,
shapes=NULL,
default.shape=NULL , style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.shape))
setNodeShapeDefault(default.shape, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genShapeMap(table.column,
network,base.url)
table.column.values<-auto.map$table.column.values
shapes<-auto.map$shapes
}
# perform mapping
mvp <- mapVisualProperty("NODE_SHAPE",table.column, 'd',
table.column.values, shapes,
network=network, base.url = base.url)
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Size Mapping
#'
#' @description Map table column values to node font sizes.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param sizes List of sizes to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.size Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @details Using this function will lock node width and height to use a
#' singular "size" value.
#' @examples \donttest{
#' setNodeSizeMapping('score')
#' setNodeSizeMapping('score', sizes=c(30,80))
#' setNodeSizeMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeSizeMapping <- function (table.column, table.column.values=NULL, sizes=NULL,
mapping.type='c', default.size=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
lockNodeDimensions(TRUE,style.name, base.url)
# set default
if(!is.null(default.size))
setNodeSizeDefault(default.size, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genDimMap('node',table.column,sizes,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
sizes<-auto.map$dims
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_SIZE",table.column, 'c',
table.column.values, sizes,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_SIZE",table.column, 'd',
table.column.values, sizes,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_SIZE",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Tooltip Mapping
#'
#' @description Pass the values from a table column to display as node tooltips.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeTooltipMapping('description')
#' }
#' @export
setNodeTooltipMapping <- function (table.column, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'node',network, base.url)) return()
mvp <- mapVisualProperty("NODE_TOOLTIP", table.column, 'p',
network = network, base.url = base.url)
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Width Mapping
#'
#' @description Map table column values to the node widths.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param widths List of width values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.width Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network.
#' Default is the "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' #' @details Using this function will unlock node width and height to use
#' separate values.
#' @examples \donttest{
#' setNodeWidthMapping('score')
#' setNodeWidthMapping('score', widths=c(30,80))
#' setNodeWidthMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeWidthMapping <- function (table.column, table.column.values=NULL, widths=NULL,
mapping.type='c', default.width=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
lockNodeDimensions(FALSE, style.name, base.url)
# set default
if(!is.null(default.width))
setNodeWidthDefault(default.width, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genDimMap('node',table.column,widths,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
widths<-auto.map$dims
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("NODE_WIDTH",table.column, 'c',
table.column.values, widths,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("NODE_WIDTH",table.column, 'd',
table.column.values, widths,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("NODE_WIDTH",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ==============================================================================
# II.b. Edge Properties
# Pattern: (1) prepare mapVisualProperty, (2) call updateStyleMapping()
# ------------------------------------------------------------------------------
#' @title Set Edge Color Mapping
#'
#' @description Map table column values to colors to set the edge color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeColorMapping <- function (table.column, table.column.values=NULL, colors=NULL,
mapping.type='c', default.color=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check for color palette use case
if(typeof(colors) == "closure"){ #i.e., name of palette function
if(is.null(table.column.values)){
auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
colors<-auto.map$colors
} else {
colors <- colors(length(table.column.values))
}
}
# check if colors are formatted correctly
for (color in colors){
.checkHexColor(color)
}
# set default
if(!is.null(default.color))
setEdgeColorDefault(default.color, style.name, base.url=base.url)
# perform mapping for COLOR (i.e., when arrowColorMatchesEdge=T)
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_UNSELECTED_PAINT",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_UNSELECTED_PAINT",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_UNSELECTED_PAINT",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
# perform mapping for STROKE (i.e., when arrowColorMatchesEdge=F)
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_STROKE_UNSELECTED_PAINT",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_STROKE_UNSELECTED_PAINT",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_STROKE_UNSELECTED_PAINT",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Font Face Mapping
#'
#' @description Sets font face for edge labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping
#' @param fonts List of string specifications of font face, style and size, e.g.,
#' c("SansSerif,plain,12", "Dialog,plain,10")
#' @param mapping.type (char) discrete or passthrough (d,p);
#' default is discrete
#' @param default.font String specification of font face, style and size, e.g.,
#' "SansSerif,plain,12" or "Dialog,plain,10"
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeFontFaceMapping("myfonts", c("normal","small"),
#' c("SansSerif,plain,12", "Dialog,plain,10"))
#' }
#' @export
setEdgeFontFaceMapping <- function(table.column, table.column.values,
fonts, mapping.type='d',
default.font=NULL,
style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'edge',network, base.url))
stop("Table column does not exist. Please try again.")
if(!is.null(default.font)){
setVisualPropertyDefault(
list(visualProperty = "EDGE_LABEL_FONT_FACE", value = default.font),
style.name, base.url)
}
if (mapping.type %in% c('continuous','c','interpolate')) {
stop("Continuous mapping of font face values is not supported.")
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp1 <- mapVisualProperty("EDGE_LABEL_FONT_FACE",table.column, 'd',
table.column.values, fonts,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp1 <- mapVisualProperty("EDGE_LABEL_FONT_FACE",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Font Size Mapping
#'
#' @description Map table column values to sizes to set the edge size.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param sizes List of sizes to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.size Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeFontSizeMapping('score')
#' setEdgeFontSizeMapping('score', sizes=c(6,24))
#' setEdgeFontSizeMapping('score', c(0,30), c(35,55))
#' }
#' @export
setEdgeFontSizeMapping <- function (table.column, table.column.values=NULL, sizes=NULL,
mapping.type='c', default.size=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.size))
setEdgeFontSizeDefault(default.size, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genDimMap('edge',table.column,sizes,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
sizes<-auto.map$dims
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_LABEL_FONT_SIZE",table.column, 'c',
table.column.values, sizes,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_LABEL_FONT_SIZE",table.column, 'd',
table.column.values, sizes,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_LABEL_FONT_SIZE",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Label Mapping
#'
#' @description Pass the values from a table column to display as edge labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLabelMapping('label')
#' }
#' @export
setEdgeLabelMapping <- function (table.column, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column, 'edge',network, base.url)) return()
mvp <- mapVisualProperty("EDGE_LABEL", table.column, 'p')
updateStyleMapping(style.name, mvp, base.url = base.url)
}
#' @export
# ------------------------------------------------------------------------------
#' @title Set Edge Label Color Mapping
#'
#' @description Map table column values to colors to set the edge border color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLabelColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeLabelColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeLabelColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeLabelColorMapping <- function (table.column, table.column.values=NULL, colors=NULL,
mapping.type='c', default.color=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check for color palette use case
if(typeof(colors) == "closure"){ #i.e., name of palette function
if(is.null(table.column.values)){
auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
colors<-auto.map$colors
} else {
colors <- colors(length(table.column.values))
}
}
# check if colors are formatted correctly
for (color in colors){
.checkHexColor(color)
}
# set default
if(!is.null(default.color))
setEdgeLabelColorDefault(default.color, style.name, base.url=base.url)
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_LABEL_COLOR",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_LABEL_COLOR",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_LABEL_COLOR",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Label Opacity Mapping
#'
#' @description Sets opacity for edge label only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLabelOpacityMapping('weight')
#' setEdgeLabelOpacityMapping('weight', opacities=c(0,100))
#' setEdgeLabelOpacityMapping('weight', c(1,10), c(50,255))
#' }
#' @export
setEdgeLabelOpacityMapping <- function(table.column, table.column.values=NULL,
opacities=NULL, mapping.type='c',
default.opacity=NULL,
style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column,'edge',network, base.url))
stop("Table column does not exist. Please try again.")
for (o in opacities){
.checkOpacity(o)
}
if(!is.null(default.opacity)){
.checkOpacity(default.opacity)
setVisualPropertyDefault(
list(visualProperty = "EDGE_LABEL_TRANSPARENCY", value = default.opacity),
style.name, base.url)
}
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genOpacityMap('edge',table.column,opacities,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
opacities<-auto.map$opacities
}
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp1 <- mapVisualProperty("EDGE_LABEL_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp1 <- mapVisualProperty("EDGE_LABEL_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp1 <- mapVisualProperty("EDGE_LABEL_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Line Style Mapping
#'
#' @description Map table column values to styles to set the edge style.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param line.styles List of line styles. Leave NULL to perform
#' an automatic mapping to available line styles. See \link{getLineStyles}.
#' @param default.line.style Style to set as default. See \link{getLineStyles}.
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLineStyleMapping('type')
#' setEdgeLineStyleMapping('type',c('pp','pd'),c('SOLID','LONG_DASH'))
#' }
#' @export
setEdgeLineStyleMapping <- function (table.column, table.column.values=NULL,
line.styles=NULL,
default.line.style='SOLID', style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.line.style))
setEdgeLineStyleDefault(default.line.style, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genLineStyleMap(table.column,
network,base.url)
table.column.values<-auto.map$table.column.values
line.styles<-auto.map$line.styles
}
# perform mapping
mvp <- mapVisualProperty("EDGE_LINE_TYPE",table.column, 'd',
table.column.values, line.styles,
network=network, base.url = base.url)
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Line Width Mapping
#'
#' @description Map table column values to widths to set the edge line width.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param widths List of width values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.width Width value to set as default for all unmapped values for all unmapped values.
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLineWidthMapping('score')
#' setEdgeLineWidthMapping('score', widths=c(1,10))
#' setEdgeLineWidthMapping('score', c(0,30), c(1,5))
#' }
#' @export
setEdgeLineWidthMapping <- function (table.column, table.column.values=NULL, widths=NULL,
mapping.type='c', default.width=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.width))
setEdgeLineWidthDefault(default.width, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genDimMap('edge',table.column,widths,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
widths<-auto.map$dims
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_WIDTH",table.column, 'c',
table.column.values, widths,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_WIDTH",table.column, 'd',
table.column.values, widths,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_WIDTH",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Opacity Mapping
#'
#' @description Map table column values to opacities to set the edge opacity.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeOpacityMapping('weight')
#' setEdgeOpacityMapping('weight', opacities=c(0,100))
#' setEdgeOpacityMapping('weight', c(1,10), c(50,255))
#' }
#' @export
setEdgeOpacityMapping <- function (table.column, table.column.values=NULL,
opacities=NULL, mapping.type='c',
default.opacity=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check if opacities are formatted correctly
for (o in opacities){
.checkOpacity(o)
}
# set default
if(!is.null(default.opacity)){
.checkOpacity(default.opacity)
setVisualPropertyDefault(
list(visualProperty = "EDGE_TRANSPARENCY", value = default.opacity),
style.name, base.url)
}
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genOpacityMap('edge',table.column,opacities,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
opacities<-auto.map$opacities
}
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_TRANSPARENCY",table.column, 'c',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_TRANSPARENCY",table.column, 'd',
table.column.values, opacities,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_TRANSPARENCY",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Target Arrow Mapping
#'
#' @description Map table column values to shapes to set the target arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTargetArrowMapping('type')
#' setEdgeTargetArrowMapping('type',c('activation','inhibition'),c('ARROW','T'))
#' }
#' @export
setEdgeTargetArrowMapping <- function (table.column, table.column.values=NULL,
shapes=NULL,
default.shape='ARROW', style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
#Whoops! Duplicate?? TODO: Deprecate?
setEdgeTargetArrowShapeMapping(table.column, table.column.values, shapes,
default.shape , style.name,
network, base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Source Arrow Mapping
#'
#' @description Map table column values to shapes to set the source arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeSourceArrowMapping('type')
#' setEdgeSourceArrowMapping('type',c('activation','inhibition'),c('ARROW','T'))
#' }
#' @export
setEdgeSourceArrowMapping <- function (table.column, table.column.values=NULL,
shapes=NULL,
default.shape='ARROW', style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
#Whoops! Duplicate?? TODO: Deprecate?
setEdgeSourceArrowShapeMapping(table.column, table.column.values, shapes,
default.shape , style.name,
network, base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Target Arrow Color Mapping
#'
#' @description Map table column values to colors to set the target arrow color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTargetArrowColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeTargetArrowColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeTargetArrowColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeTargetArrowColorMapping <- function (table.column, table.column.values=NULL, colors=NULL,
mapping.type='c', default.color=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check for color palette use case
if(typeof(colors) == "closure"){ #i.e., name of palette function
if(is.null(table.column.values)){
auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
colors<-auto.map$colors
} else {
colors <- colors(length(table.column.values))
}
}
# check if colors are formatted correctly
for (color in colors){
.checkHexColor(color)
}
# set default
if(!is.null(default.color))
setEdgeTargetArrowColorDefault(default.color, style.name, base.url=base.url)
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_TARGET_ARROW_UNSELECTED_PAINT",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_TARGET_ARROW_UNSELECTED_PAINT",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_TARGET_ARROW_UNSELECTED_PAINT",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Source Arrow Color Mapping
#'
#' @description Map table column values to colors to set the source arrow color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p);
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is
#' http://localhost:1234 and the latest version of the CyREST API supported by
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeSourceArrowColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeSourceArrowColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeSourceArrowColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeSourceArrowColorMapping <- function (table.column, table.column.values=NULL, colors=NULL,
mapping.type='c', default.color=NULL, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# check for color palette use case
if(typeof(colors) == "closure"){ #i.e., name of palette function
if(is.null(table.column.values)){
auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
network,base.url)
table.column.values<-auto.map$table.column.values
colors<-auto.map$colors
} else {
colors <- colors(length(table.column.values))
}
}
# check if colors are formatted correctly
for (color in colors){
.checkHexColor(color)
}
# set default
if(!is.null(default.color))
setEdgeSourceArrowColorDefault(default.color, style.name, base.url=base.url)
# perform mapping
if (mapping.type %in% c('continuous','c','interpolate')) {
mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_UNSELECTED_PAINT",table.column, 'c',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('discrete','d','lookup')){
mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_UNSELECTED_PAINT",table.column, 'd',
table.column.values, colors,
network=network, base.url = base.url)
} else if (mapping.type %in% c('passthrough','p')){
mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_UNSELECTED_PAINT",table.column, 'p',
network=network, base.url = base.url)
} else {
stop("mapping.type not recognized.")
}
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Target Arrow Shape Mapping
#'
#' @description Map table column values to shapes to set the target arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTargetArrowShapeMapping('type')
#' setEdgeTargetArrowShapeMapping('type',c('activation','inhibition'),
#' c('ARROW','T'))
#' }
#' @export
setEdgeTargetArrowShapeMapping <- function(table.column,
table.column.values=NULL, shapes=NULL,
default.shape=NULL , style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.shape))
setEdgeTargetArrowShapeDefault(default.shape, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genArrowMap(table.column,
network,base.url)
table.column.values<-auto.map$table.column.values
shapes<-auto.map$shapes
}
# perform mapping
mvp <- mapVisualProperty("EDGE_TARGET_ARROW_SHAPE",table.column, 'd',
table.column.values, shapes,
network=network, base.url = base.url)
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Source Arrow Shape Mapping
#'
#' @description Map table column values to shapes to set the source arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeSourceArrowShapeMapping('type')
#' setEdgeSourceArrowShapeMapping('type',c('activation','inhibition'),
#' c('ARROW','T'))
#' }
#' @export
setEdgeSourceArrowShapeMapping <- function(table.column,
table.column.values=NULL, shapes=NULL,
default.shape=NULL , style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
# set default
if(!is.null(default.shape))
setEdgeSourceArrowShapeDefault(default.shape, style.name, base.url=base.url)
# check table.column.values to map
if(is.null(table.column.values)){
auto.map<-.genArrowMap(table.column,
network,base.url)
table.column.values<-auto.map$table.column.values
shapes<-auto.map$shapes
}
# perform mapping
mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_SHAPE",table.column, 'd',
table.column.values, shapes,
network=network, base.url = base.url)
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Tooltip Mapping
#'
#' @description Pass the values from a table column to display as edge tooltips.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current"
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTooltipMapping('description')
#' }
#' @export
setEdgeTooltipMapping <- function (table.column, style.name=NULL,
network=NULL, base.url=.defaultBaseUrl) {
if(!.tableColumnExists(table.column, 'edge',network, base.url)) return()
mvp <- mapVisualProperty("EDGE_TOOLTIP", table.column, 'p')
updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ==============================================================================
# III. Palette property value generators
# ------------------------------------------------------------------------------
#'@export
# ------------------------------------------------------------------------------
#' @title paletteColorRandom Qualitative
#'
#' @description Generate a qualitative random color map of a given size
#' @param value.count Number of colors to generate; default is 1
#' @return List of random colors
#' @examples
#' paletteColorRandom()
#' @seealso genNodeColorMap genEdgeColorMap
#' @export
paletteColorRandom<-function(value.count=1){
rgb(sample(0:255,size=value.count,replace=TRUE),
sample(0:255,size=value.count,replace=TRUE),
sample(0:255,size=value.count,replace=TRUE),
maxColorValue=255)
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPastel2 Qualitative
#'
#' @description Generate a qualitative Pastel2 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPastel2()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPastel2<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Pastel2'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPastel1 Qualitative
#'
#' @description Generate a qualitative Pastel1 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPastel1()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPastel1<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Pastel1'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerDark2 Qualitative
#'
#' @description Generate a qualitative Dark2 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerDark2()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerDark2<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Dark2'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerAccent Qualitative
#'
#' @description Generate a qualitative Accent Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerAccent()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerAccent<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Accent'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPaired Qualitative
#'
#' @description Generate a qualitative Paired Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is
#' 12. See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPaired()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPaired<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Paired'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerSet1 Qualitative
#'
#' @description Generate a qualitative Set1 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerSet1()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerSet1<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Set1'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerSet2 Qualitative
#'
#' @description Generate a qualitative Set2 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerSet2()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerSet2<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Set2'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerSet3 Qualitative
#'
#' @description Generate a qualitative Set3 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is
#' 12. See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerSet3()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerSet3<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Set3'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlOrRd Sequential
#'
#' @description Generate a sequential YlOrRd Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlOrRd()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlOrRd<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'YlOrRd'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlOrBr Sequential
#'
#' @description Generate a sequential YlOrBr Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlOrBr()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlOrBr<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'YlOrBr'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlGnBu Sequential
#'
#' @description Generate a sequential YlGnBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlGnBu()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlGnBu<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'YlGnBu'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlGn Sequential
#'
#' @description Generate a sequential YlGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlGn()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlGn<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'YlGn'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerReds Sequential
#'
#' @description Generate a sequential Reds Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerReds()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerReds<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Reds'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerRdPu Sequential
#'
#' @description Generate a sequential RdPu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerRdPu()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerRdPu<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'RdPu'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPurples Sequential
#'
#' @description Generate a sequential Purples Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPurples()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPurples<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Purples'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuRd Sequential
#'
#' @description Generate a sequential PuRd Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuRd()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuRd<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'PuRd'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuBuGn Sequential
#'
#' @description Generate a sequential PuBuGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuBuGn()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuBuGn<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'PuBuGn'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuBu Sequential
#'
#' @description Generate a sequential PuBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuBu()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuBu<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'PuBu'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerOrRd Sequential
#'
#' @description Generate a sequential OrRd Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerOrRd()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerOrRd<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'OrRd'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerOranges Sequential
#'
#' @description Generate a sequential Oranges Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerOranges()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerOranges<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Oranges'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerGreys Sequential
#'
#' @description Generate a sequential Greys Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerGreys()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerGreys<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Greys'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerGreens Sequential
#'
#' @description Generate a sequential Greens Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerGreens()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerGreens<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Greens'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerGnBu Sequential
#'
#' @description Generate a sequential GnBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerGnBu()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerGnBu<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'GnBu'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBuPu Sequential
#'
#' @description Generate a sequential BuPu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerBuPu()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBuPu<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'BuPu'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBuGn Sequential
#'
#' @description Generate a sequential BuGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerBuGn()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBuGn<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'BuGn'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBlues Sequential
#'
#' @description Generate a sequential Blues Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerBlues()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBlues<-function(value.count=3) {
return(RColorBrewer::brewer.pal(value.count, 'Blues'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerRdYlBu Divergent
#'
#' @description Generate a divergent RdYlBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerRdYlBu()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerRdYlBu<-function(value.count=3) {
return(rev(RColorBrewer::brewer.pal(value.count, 'RdYlBu')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerRdBu Divergent
#'
#' @description Generate a divergent RdBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerRdBu()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerRdBu<-function(value.count=3) {
return(rev(RColorBrewer::brewer.pal(value.count, 'RdBu')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuOr Divergent
#'
#' @description Generate a divergent PuOr Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuOr()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuOr<-function(value.count=3) {
return(rev(RColorBrewer::brewer.pal(value.count, 'PuOr')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPRGn Divergent
#'
#' @description Generate a divergent PRGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPRGn()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPRGn<-function(value.count=3) {
return(rev(RColorBrewer::brewer.pal(value.count, 'PRGn')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPiYG Divergent
#'
#' @description Generate a divergent PiYG Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPiYG()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPiYG<-function(value.count=3) {
return(rev(RColorBrewer::brewer.pal(value.count, 'PiYG')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBrBG Divergent
#'
#' @description Generate a divergent BrBG Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerBrBG()
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBrBG<-function(value.count=3) {
return(rev(RColorBrewer::brewer.pal(value.count, 'BrBG')))
}
# ==============================================================================
# III.a Internal mapping generators
# ------------------------------------------------------------------------------
# Automatic construction of table.column.values for mapping
.autoTableColumnValues<-function(table=NULL,
table.column=NULL,
mapping.type=NULL,
network=NULL,
base.url=.defaultBaseUrl){
# Find out all of the values in the named column
df.values = getTableColumns(table=table, columns=table.column,
network=network, base.url=base.url)
if(mapping.type == 'd'){
# Find the frequency distribution, with most common elements first
# Note: not same ordering as Cytoscape
df.freq = table(df.values[table.column])
# Create the mapped values that correspond to the unique elements
return(names(df.freq))
} else if (mapping.type == 'c'){
#Determine min and max
max.value <- max(df.values,na.rm=TRUE)
min.value <- min(df.values,na.rm=TRUE)
if(sign(max.value) == sign(min.value)){ #one-tailed; seq
mid.value = min.value + (max.value - min.value)/2
return(c(min.value,mid.value,max.value))
} else { #two-tailed; div
#Find max abs value
max.max.value <- max(max.value, abs(min.value))
return(c(-max.max.value, 0, max.max.value))
}
} else {
stop("Automatic palette mapping doesn't work for passthrough mappings.")
}
}
# Internal function to generate a color map
# param table Node, Edge or Network table
# param table.column Name of column
# param color.palette Name of palette function (without quotes)
# param mapping.type (char) continuous, discrete or passthrough (c,d,p);
# default is continuous
# param network (optional) Name or SUID of the network. Default is the
# "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
# port or version to connect to the CyREST API. Default is
# http://localhost:1234 and the latest version of the CyREST API supported by
# this version of RCy3.
# return A named list of lists providing a mapping of column values and colors
.genColorMap<-function(table=NULL,
table.column=NULL,
color.palette=NULL,
mapping.type=NULL,
network=NULL,
base.url=.defaultBaseUrl){
table.column.values <- .autoTableColumnValues(table, table.column,
mapping.type,network, base.url)
colors <- color.palette(length(table.column.values))
return (list('table.column.values'=table.column.values, 'colors'=colors))
}
# ------------------------------------------------------------------------------
# Internal function to generate an opacity map
# param table Node, Edge or Network table
# param table.column Name of column
# param opacities Range of opacity values to work with; default is 50-255
# param mapping.type (char) continuous, discrete or passthrough (c,d,p);
# default is continuous
# param network (optional) Name or SUID of the network. Default is the
# "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
# port or version to connect to the CyREST API. Default is
# http://localhost:1234 and the latest version of the CyREST API supported by
# this version of RCy3.
# return A named list of lists providing a mapping of column values and opacities
.genOpacityMap<-function(table=NULL,
table.column=NULL,
opacities=NULL,
mapping.type=NULL,
network=NULL,
base.url=.defaultBaseUrl){
table.column.values <- .autoTableColumnValues(table, table.column,
mapping.type,network, base.url)
if(is.null(opacities))
opacities <- c(50,255) #default range
if(length(opacities) > 2){
warning("More than 2 opacity values provided. Only using min and max.")
opacities <- c(min(opacities), max(opacities))
}else if (length(opacities) < 2){
stop("Please provide min and max opacity values between from 0 to 255")
}
opacities <- seq(min(opacities), max(opacities), along.with = table.column.values)
return (list('table.column.values'=table.column.values, 'opacities'=opacities))
}
# ------------------------------------------------------------------------------
# Internal function to generate a dimensions map
# param table Node, Edge or Network table
# param table.column Name of column
# param dims Range of dimension values to work with; default is 10-100
# param mapping.type (char) continuous, discrete or passthrough (c,d,p);
# default is continuous
# param network (optional) Name or SUID of the network. Default is the
# "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
# port or version to connect to the CyREST API. Default is
# http://localhost:1234 and the latest version of the CyREST API supported by
# this version of RCy3.
# return A named list of lists providing a mapping of column values and
# dimension values
.genDimMap<-function(table=NULL,
table.column=NULL,
dims=NULL,
mapping.type=NULL,
network=NULL,
base.url=.defaultBaseUrl){
table.column.values <- .autoTableColumnValues(table, table.column,
mapping.type,network, base.url)
if(is.null(dims))
dims <- c(10,100) #default range
if(length(dims) > 2){
warning("More than 2 dimension values provided. Only using min and max.")
dims <- c(min(dims), max(dims))
}else if (length(dims) < 2){
stop("Please provide min and max dimension values.")
}
dims <- seq(min(dims), max(dims), along.with = table.column.values)
return (list('table.column.values'=table.column.values, 'dims'=dims))
}
# ------------------------------------------------------------------------------
# Internal function to generate a line style map
# param table.column Name of column
# param network (optional) Name or SUID of the network. Default is the
# "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
# port or version to connect to the CyREST API. Default is
# http://localhost:1234 and the latest version of the CyREST API supported by
# this version of RCy3.
# return A named list of lists providing a mapping of column values and line
# styles
.genLineStyleMap<-function(table.column=NULL,
network=NULL,
base.url=.defaultBaseUrl){
table.column.values <- .autoTableColumnValues('edge', table.column,
'd',network, base.url)
value.count <- length(table.column.values)
if(value.count > 16)
stop("A maximum of 16 line styles are available.")
line.styles <- getLineStyles()[1:value.count]
return (list('table.column.values'=table.column.values, 'line.styles'=line.styles))
}
# ------------------------------------------------------------------------------
# Internal function to generate an arrow shape map
# param table.column Name of column
# param network (optional) Name or SUID of the network. Default is the
# "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
# port or version to connect to the CyREST API. Default is
# http://localhost:1234 and the latest version of the CyREST API supported by
# this version of RCy3.
# return A named list of lists providing a mapping of column values and arrow
# shapes
.genArrowMap<-function(table.column=NULL,
network=NULL,
base.url=.defaultBaseUrl){
table.column.values <- .autoTableColumnValues('edge', table.column,
'd',network, base.url)
value.count <- length(table.column.values)
if(value.count > 22)
stop("A maximum of 22 ArrowShapes are available.")
shapes <- getArrowShapes()[1:value.count]
return (list('table.column.values'=table.column.values, 'shapes'=shapes))
}
# ------------------------------------------------------------------------------
# Internal function to generate a shape map
# param table.column Name of column
# param network (optional) Name or SUID of the network. Default is the
# "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
# port or version to connect to the CyREST API. Default is
# http://localhost:1234 and the latest version of the CyREST API supported by
# this version of RCy3.
# return A named list of lists providing a mapping of column values and shapes
.genShapeMap<-function(table.column=NULL,
network=NULL,
base.url=.defaultBaseUrl){
table.column.values <- .autoTableColumnValues('node', table.column,
'd',network, base.url)
value.count <- length(table.column.values)
if(value.count > 9)
stop("A maximum of 9 shapes are available.")
shapes <- getNodeShapes()[1:value.count]
return (list('table.column.values'=table.column.values, 'shapes'=shapes))
}
