#' The 'boilerplate' for this package's desired graph style
#' @description Generates an object that can be converted to a JSON file
#' and subsequently applied to the graph for the markup specified by this
#' package and the layout mirroring KEGG.
#' Intended for use within \code{\link{cyto_vis}}
#' @export
#' @param style_name An argument to name style; when used inside
#' of \code{\link{cyto_vis}} no name is needed
#' @param map_edge_width A logical indicator; if FALSE no continuous mapping
#' of edge width will be applied
#' @param edge_width_attribute The attribute that will be used for edge width;
#' if data is not added or the attribute is not part of the graphing
#' information, the edge width will default to 1.
#' @param min_score The minimum attribute value for the column used to map
#' edge width
#' @param max_score The maximum attribute value for the column used to map
#' edge width
#' @return A list that can be converted to a JSON file to apply desired
#' style/layout in Cytoscape
#' @examples
#' style.name = "myKEGGstyle"
#' mappings <- generate_mappings(style.name, FALSE)
generate_mappings <-
function(style_name, map_edge_width, edge_width_attribute,
min_score, max_score){
style.name = style_name
# Visual Mappings
#######
##defaults
def.node.font <- list(visualProperty = "NODE_LABEL_FONT_FACE",
value = "TeXGyrePagella-Regular")
defaults <- list(def.node.font)
#######
####transparency
pair1a = list(key = "group",value = "0")
pair1b = list(key = "gene", value = "150")
pair1c = list(key = "compound", value = "255")
pair1d = list(key = "map",value = "255")
discrete.mappings.1 = list(pair1a, pair1b, pair1c, pair1d)
####node shape
pair2a = list(key = "circle", value = "Ellipse")
pair2b = list(key = "roundrectangle", value = "Round_Rectangle")
pair2c = list(key = "rectangle", value = "Rectangle")
discrete.mappings.2 = list(pair2a, pair2b, pair2c)
###edge target arrow shape
pair3a = list(key = "activation", value = "Delta")
pair3b = list(key = "expression", value = "Arrow")
pair3c = list(key = "indirect_effect", value = "Diamond")
pair3d = list(key = "inhibition", value = "T")
pair3e = list(key = "inhibition_phosphorylation", value = "T")
pair3f = list(key = "irreversible", value = "Arrow")
pair3g = list(key = "phosphorylation", value = "Diamond")
pair3h = list(key = "repression", value = "T")
discrete.mappings.3 = list(pair3a, pair3b, pair3c, pair3d, pair3e, pair3f,
pair3g, pair3h)
###node label location
pair4a = list(key = "compound", value = "S,N,c,0.0,0.0")
pair4b = list(key = "group", value = "E,W,c,2.0,0.0")
discrete.mappings.4 = list(pair4a, pair4b)
###dashed edge for indirect effects
pair5 = list(key = "0.0", value = "Equal_Dash")
discrete.mappings.5 = list(pair5)
###transparancy for edges [based on existence in data :
### not needed for 'default' graphs]
pair6a = list(key = "0.0",value = "100")
pair6b = list(key = "1.0", value = "255")
discrete.mappings.6 = list(pair6a, pair6b)
node.transparency = list(mappingType="discrete",
mappingColumn="entryTYPE",
mappingColumnType="String",
visualProperty="NODE_TRANSPARENCY",
map = discrete.mappings.1)
node.shape = list(mappingType="discrete",
mappingColumn="shape",
mappingColumnType="String",
visualProperty="NODE_SHAPE",
map = discrete.mappings.2)
node.label.position = list(mappingType="discrete",
mappingColumn="entryTYPE",
mappingColumnType="String",
visualProperty="NODE_LABEL_POSITION",
map = discrete.mappings.4)
node.color = list(mappingType="passthrough",
mappingColumn="BGcolor",
mappingColumnType="String",
visualProperty="NODE_FILL_COLOR")
node.label = list(mappingType="passthrough",
mappingColumn="LABEL",
mappingColumnType="String",
visualProperty="NODE_LABEL")
node.label.width = list(mappingType="passthrough",
mappingColumn="width",
mappingColumnType="String",
visualProperty="NODE_LABEL_WIDTH")
node.Xcoord = list(mappingType="passthrough",
mappingColumn="Xcoord",
mappingColumnType="Double",
visualProperty="NODE_X_LOCATION")
node.Ycoord = list(mappingType="passthrough",
mappingColumn="Ycoord",
mappingColumnType="Double",
visualProperty="NODE_Y_LOCATION")
node.width = list(mappingType="passthrough",
mappingColumn="width",
mappingColumnType="Double",
visualProperty="NODE_WIDTH")
node.height = list(mappingType="passthrough",
mappingColumn="height",
mappingColumnType="Double",
visualProperty="NODE_HEIGHT")
node.border.width = list(mappingType="passthrough",
mappingColumn="border_width",
mappingColumnType="Double",
visualProperty="NODE_BORDER_WIDTH")
node.label.font.size = list(mappingType="passthrough",
mappingColumn="label_font_size",
mappingColumnType="Double",
visualProperty="NODE_LABEL_FONT_SIZE")
node.tooltip = list(mappingType="passthrough",
mappingColumn="entryNAMES",
mappingColumnType="String",
visualProperty="NODE_TOOLTIP")
node.mappings = list(node.color, node.label, node.label.width,
node.label.position, node.border.width,node.Xcoord,
node.Ycoord, node.width, node.height,
node.transparency, node.shape, node.label.font.size,
node.tooltip)
edge.target.arrow.shape = list(mappingType="discrete",
mappingColumn="subtype1",
mappingColumnType="String",
visualProperty="EDGE_TARGET_ARROW_SHAPE",
map = discrete.mappings.3)
edge.line.type = list(mappingType="discrete",
mappingColumn="is_direct",
mappingColumnType="Double",
visualProperty="EDGE_LINE_TYPE",
map = discrete.mappings.5)
edge.transparency = list(mappingType="discrete",
mappingColumn="has_data",
mappingColumnType="Double",
visualProperty="EDGE_TRANSPARENCY",
map = discrete.mappings.6)
edge.target.arrow.color = list(mappingType="passthrough",
mappingColumn="color",
mappingColumnType="String",
visualProperty=
"EDGE_TARGET_ARROW_UNSELECTED_PAINT")
edge.label = list(mappingType="passthrough",
mappingColumn="edge_label",
mappingColumnType="String",
visualProperty="EDGE_LABEL")
edge.color = list(mappingType="passthrough",
mappingColumn="color",
mappingColumnType="String",
visualProperty="EDGE_STROKE_UNSELECTED_PAINT")
edge.tooltip = list(mappingType="passthrough",
mappingColumn="tooltip",
mappingColumnType="String",
visualProperty="EDGE_TOOLTIP")
if (map_edge_width){
point1 = list(value=min_score, lesser= "1", equal="1", greater="1")
point2 = list(value=max_score, lesser="20", equal="20", greater="20")
edge.width.continuous.points = list(point1, point2)
edge.width = list(mappingType="continuous",
mappingColumn = edge_width_attribute,
mappingColumnType="Double",
visualProperty="EDGE_WIDTH",
points = edge.width.continuous.points)
edge.mappings = list(edge.target.arrow.color, edge.target.arrow.shape,
edge.line.type, edge.color, edge.tooltip,
edge.label, edge.transparency, edge.width)
}
else {
edge.mappings = list(edge.target.arrow.color, edge.target.arrow.shape,
edge.line.type, edge.color,
edge.tooltip, edge.label)
}
mappings <- c(node.mappings, edge.mappings)
return(list(defaults,mappings))
}
