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##' annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label
##'
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##'
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##' @title geom_strip
##' @param taxa1 taxa1
##' @param taxa2 taxa2
##' @param label optional label
##' @param offset offset of bar and text from the clade
##' @param offset.text offset of text from bar
##' @param align logical
##' @param barsize size of bar
##' @param barextend extend bar vertically
##' @param fontsize size of text
##' @param angle angle of text
##' @param geom one of 'text' or 'label'
##' @param hjust hjust
##' @param fill fill label background, only work with geom='label'
##' @param family sans by default, can be any supported font
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##' @param parse logical, whether parse label
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##' @param ... additional parameter
##' @return ggplot layers
##' @export
##' @author Guangchuang Yu
geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,
align=TRUE, barsize=0.5, barextend=0, fontsize=3.88,
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angle=0, geom="text", hjust=0, fill=NA, family="sans",
parse=FALSE, ...) {
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mapping <- NULL
data <- NULL
position <- "identity"
show.legend <- NA
na.rm <- TRUE
inherit.aes <- FALSE
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layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset, align=align,
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size=barsize, barextend=barextend,
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mapping=mapping, data=data,
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position=position, show.legend = show.legend,
inherit.aes = inherit.aes, na.rm=na.rm, ...)
if (is.na(label) || is.null(label)) {
return(layer_bar)
}
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if (geom == "text") {
## no fill parameter
layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,
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align=align, size=fontsize, barextend=barextend, angle=angle, family=family,
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mapping=mapping, data=data, geom=geom, hjust=hjust,
position=position, show.legend = show.legend,
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inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)
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} else {
layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,
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align=align, size=fontsize, barextend=barextend, angle=angle, fill=fill,family=family,
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mapping=mapping, data=data, geom=geom, hjust=hjust,
position=position, show.legend = show.legend,
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inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)
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}
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list(
layer_bar,
layer_text
)
}
stat_stripText <- function(mapping=NULL, data=NULL,
geom="text", position="identity",
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taxa1, taxa2, label, offset, align, barextend, ...,
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show.legend=NA, inherit.aes=FALSE, na.rm=FALSE, parse=FALSE) {
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if (is.null(label) || is.na(label)) {
default_aes <- aes_(x=~x, y=~y, node=~node, label=~label)
} else {
default_aes <- aes_(x=~x, y=~y, node=~node)
}
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if (is.null(mapping)) {
mapping <- default_aes
} else {
mapping <- modifyList(mapping, default_aes)
}
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layer(stat=StatStripText,
data=data,
mapping=mapping,
geom=geom,
position=position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params=list(taxa1=taxa1,
taxa2=taxa2,
label=label,
offset=offset,
align=align,
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barextend=barextend,
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na.rm=na.rm,
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parse=parse,
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...),
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check.aes = FALSE
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)
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}
stat_stripBar <- function(mapping=NULL, data=NULL,
geom="segment", position="identity",
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taxa1, taxa2, label=label, offset, align, barextend, ...,
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show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
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if (is.null(label) || is.na(label)) {
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default_aes <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y)
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} else {
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default_aes <- aes_(x=~x, y=~y, node=~node, xend=~x, yend=~y)
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}
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if (is.null(mapping)) {
mapping <- default_aes
} else {
mapping <- modifyList(mapping, default_aes)
}
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layer(stat=StatStripBar,
data=data,
mapping=mapping,
geom=geom,
position=position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params=list(taxa1=taxa1,
taxa2=taxa2,
offset=offset,
align=align,
barextend=barextend,
na.rm=na.rm,
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...),
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check.aes = FALSE
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)
}
StatStripText <- ggproto("StatStripText", Stat,
compute_group = function(self, data, scales, params, taxa1, taxa2,
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label, offset, align, barextend) {
df <- get_striplabel_position(data, taxa1, taxa2, offset, align, barextend, adjustRatio = 1.03)
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df$y <- mean(c(df$y, df$yend))
df$label <- label
return(df)
},
required_aes = c("x", "y", "label")
)
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StatStripBar <- ggproto("StatStripBar", Stat,
compute_group = function(self, data, scales, params,
taxa1, taxa2, offset, align, barextend) {
get_striplabel_position(data, taxa1, taxa2, offset, align, barextend, adjustRatio=1.02)
},
required_aes = c("x", "y", "xend", "yend")
)
get_striplabel_position <- function(data, taxa1, taxa2, offset, align, barextend, adjustRatio) {
df <- get_striplabel_position_(data, taxa1, taxa2, barextend)
if (align) {
mx <- max(data$x, na.rm=TRUE)
} else {
mx <- df$x
}
mx <- mx * adjustRatio + offset
data.frame(x=mx, xend=mx, y=df$y, yend=df$yend)
}
get_striplabel_position_ <- function(data, taxa1, taxa2, barextend=0) {
node1 <- taxa2node(data, taxa1)
node2 <- taxa2node(data, taxa2)
xx <- with(data, c(x[node == node1], x[node == node2]))
yy <- with(data, c(y[node == node1], y[node == node2]))
data.frame(x=max(xx), y=min(yy)-barextend, yend=max(yy)+barextend)
}
## used in geom_strip, geom_taxalink
taxa2node <- function(data, taxa) {
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if (! 'label' %in% colnames(data))
data$label <- NA
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idx <- with(data, which(taxa == label | taxa == node))
if (length(idx) == 0) {
stop("input taxa is not valid...")
}
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return(data$node[idx])
}
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|
