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R/xEnrichCtree.r
In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Defines functions
xEnrichCtree
Documented in
xEnrichCtree
#' Function to visualise enrichment results using a tree-like circular plot
#'
#' \code{xEnrichCtree} is supposed to visualise enrichment results using a tree-like circular plot.
#'
#' @param eTerm an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having all these columns ('name','adjp','or','zscore','nOverlap'; 'group' optionally)
#' @param ig an object of class "igraph" with node attribute 'name'. It could be a 'phylo' object converted to. Note: the leave labels would be the node attribute 'name' unless the node attribute 'label' is explicitely provided
#' @param FDR.cutoff FDR cutoff used to show the significant terms only. By default, it is set to NULL; useful when nodes sized by FDR
#' @param node.color which statistics will be used for node coloring. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score
#' @param colormap short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in \url{http://html-color-codes.info/color-names}
#' @param zlim the minimum and maximum values for which colors should be plotted
#' @param node.size which statistics will be used for node size. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score
#' @param slim the minimum and maximum values for which sizes should be plotted
#' @param node.size.range the range of actual node size
#' @param group.gap the gap between group circles. Only works when multiple groups provided
#' @param group.color the color of group circles. Only works when multiple groups provided
#' @param group.size the line width of group circles. Only works when multiple groups provided
#' @param group.label.size the size of group circle labelling. Always a sequential integer located at the top middle. Only works when multiple groups provided
#' @param group.label.color the color of group circle labelling. Only works when multiple groups provided
#' @param legend.direction the legend guide direction. It can be "horizontal" (useful for many groups with lengthy labelling), "vertical" and "auto" ("vertical" when multiple groups provided; otherwise "horizontal")
#' @param leave.label.orientation the leave label orientation. It can be "outwards" and "inwards"
#' @param ... additional graphic parameters used in xCtree
#' @return
#' a ggplot2 object appended with 'ig', 'data' which should contain columns 'x','y', 'leaf' (T/F), 'name' (the same as V(ig)$name), 'tipid' (tip id), 'label' (if not given in ig, a 'name' varient), 'angle' and 'hjust' (assist in leave label orientation), and 'data_enrichment' (enrichment results for tips)
#' @note none
#' @export
#' @seealso \code{\link{xCtree}}
#' @include xEnrichCtree.r
#' @examples
#' \dontrun{
#' # Load the XGR package and specify the location of built-in data
#' library(XGR)
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
#'
#' # load the atlas of AA pathways
#' AA.template <- xRDataLoader("AA.template", RData.location=RData.location)
#' # consensus tree
#' ig <- AA.template$consensus$ig
#'
#' # enrichment analysis using AA pathways
#' input <- xRDataLoader('Haploid_regulators_all', RData.location=RData.location)
#' data <- subset(input, Phenotype=="AKT")
#' genes <- data$Gene[data$FDR<0.05]
#' background <- data$Gene
#' eTerm <- xEnricherGenes(genes, background=background, ontology="AA", min.overlap=5, test="fisher", RData.location=RData.location)
#'
#' # circular visualisation of enriched AA pathways
#' gp <- xEnrichCtree(eTerm, ig)
#'
#' ###############################
#' # advanced use: multiple groups
#' # enrichment analysis using AA pathways
#' Haploid <- subset(input, FDR<0.05)
#' ls_group <- split(x=Haploid$Gene, f=Haploid$Phenotype)
#' background <- unique(input$Gene)
#' ls_eTerm <- xEnricherGenesAdv(ls_group, background=background, ontologies="AA", test="fisher", min.overlap=5, RData.location=RData.location)
#'
#' # circular visualisation of enriched AA pathways
#' gp <- xEnrichCtree(ls_eTerm, ig)
#' }
xEnrichCtree <- function(eTerm, ig, FDR.cutoff=NULL, node.color=c("zscore","adjp","or","nOverlap"), colormap="brewer.Reds", zlim=NULL, node.size=c("adjp","zscore","or","nOverlap"), slim=NULL, node.size.range=c(0.5,4.5), group.gap=0.08, group.color="lightblue", group.size=0.2, group.label.size=2, group.label.color="black", legend.direction=c("auto","horizontal","vertical"), leave.label.orientation=c('inwards','outwards'), ...)
{
## match.arg matches arg against a table of candidate values as specified by choices, where NULL means to take the first one
node.color <- match.arg(node.color)
node.size <- match.arg(node.size)
legend.direction <- match.arg(legend.direction)
leave.label.orientation <- match.arg(leave.label.orientation)
if(is.null(eTerm)){
warnings("There is no enrichment in the 'eTerm' object.\n")
return(NULL)
}
if(class(ig)!="igraph"){
warnings("The 'ig' object must be provided.\n")
return(NULL)
}else{
if(!("name" %in% igraph::vertex_attr_names(ig))){
warnings("The 'ig' object must contain a node attribute 'name'.\n")
return(NULL)
}
}
if(class(eTerm)=='eTerm'){
df_enrichment_group <- xEnrichViewer(eTerm, top_num="all")
df_enrichment_group$group <- 'group'
}else if(class(eTerm)=='ls_eTerm' | class(eTerm)=='data.frame'){
if(class(eTerm)=='ls_eTerm'){
df_enrichment_group <- eTerm$df
}else if(class(eTerm)=='data.frame'){
if(all(c('group','name','adjp','or','zscore','nOverlap') %in% colnames(eTerm))){
df_enrichment_group <- eTerm[,c('group','name','adjp','or','zscore','nOverlap')]
}else if(all(c('name','adjp','or','zscore','nOverlap') %in% colnames(eTerm))){
df_enrichment_group <- eTerm[,c('name','adjp','or','zscore','nOverlap')]
df_enrichment_group$group <- 'group'
}
}
}
##########
# force those insignificant (FDR) to 1; useful when nodes sized by FDR
if(!is.null(FDR.cutoff)){
df_enrichment_group$adjp[df_enrichment_group$adjp>=FDR.cutoff] <- 1
}
##########
if(class(df_enrichment_group$group)=='factor'){
if(length(unique(df_enrichment_group$group)) != length(levels(df_enrichment_group$group))){
df_enrichment_group$group <- factor(df_enrichment_group$group, levels=sort(unique(df_enrichment_group$group)))
}
}
gp <- NULL
if(class(ig)=="igraph"){
#########################
## replace those infinite
df_enrichment_group$or[is.infinite(df_enrichment_group$or)] <- max(df_enrichment_group$or[!is.infinite(df_enrichment_group$or)])
#########################
# convert 'ig' into 'ls_igg' by group
ls_df <- split(x=df_enrichment_group[,c("name","zscore","adjp","or","nOverlap")], f=df_enrichment_group$group)
ls_igg <- lapply(ls_df, function(df_enrichment){
igg <- ig
V(igg)$zscore <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$zscore[!is.na(ind)] <- df_enrichment$zscore[ind[!is.na(ind)]]
V(igg)$adjp <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$adjp[!is.na(ind)] <- -1*log10(df_enrichment$adjp)[ind[!is.na(ind)]]
V(igg)$or <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$or[!is.na(ind)] <- log2(df_enrichment$or)[ind[!is.na(ind)]]
V(igg)$nOverlap <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$nOverlap[!is.na(ind)] <- df_enrichment$nOverlap[ind[!is.na(ind)]]
igg
})
if(node.color=="or"){
node.color.title <- expression(log[2](OR))
if(is.null(zlim)){
zlim <- c(0, ceiling(max(log2(df_enrichment_group$or))))
}
}else if(node.color=="adjp"){
node.color.title <- expression(-log[10](FDR))
if(is.null(zlim)){
zlim <- c(0, ceiling(max(-1*log10(df_enrichment_group$adjp))))
}
}else if(node.color=="zscore"){
node.color.title <- "Z-score"
if(is.null(zlim)){
zlim <- c(0, ceiling(max(df_enrichment_group$zscore)))
}
}else if(node.color=="nOverlap"){
node.color.title <- "# genes"
if(is.null(zlim)){
zlim <- c(0, ceiling(max(df_enrichment_group$nOverlap)))
}
}
if(node.size=="or"){
node.size.title <- expression(log[2](OR))
if(is.null(slim)){
slim <- c(0, ceiling(max(log2(df_enrichment_group$or))))
}
}else if(node.size=="adjp"){
node.size.title <- expression(-log[10](FDR))
if(is.null(slim)){
slim <- c(0, ceiling(max(-1*log10(df_enrichment_group$adjp))))
}
}else if(node.size=="zscore"){
node.size.title <- "Z-score"
if(is.null(slim)){
slim <- c(0, ceiling(max(df_enrichment_group$zscore)))
}
}
else if(node.size=="nOverlap"){
node.size.title <- "Num of genes"
if(is.null(slim)){
slim <- c(0, ceiling(max(df_enrichment_group$nOverlap)))
}
}
x <- y <- leaf <- x_group <- y_group <- group <- group_id <- color <- size <- NULL
if(length(ls_igg)>1){
leave.label.orientation <- 'inwards'
}
gp <- xCtree(ig, leave.label.orientation=leave.label.orientation, ...)
df_tips <- subset(gp$data, leaf==T)
ls_df <- lapply(1:length(ls_igg), function(i){
g <- ls_igg[[i]]
if(length(ls_igg)<10){
# 0-leading
group <- paste0(i, ": ", names(ls_igg)[i])
group_id <- i
}else{
group <- sprintf("%02d: %s", i, names(ls_igg)[i])
group_id <- sprintf("%02d", i)
}
x_group <- 1.05+(i-1)*group.gap
y_group <- 1.05+(i-1)*group.gap
ind <- match(V(g)$name, df_tips$name)
if(node.color=="or"){
color <- V(g)$or[!is.na(ind)]
}else if(node.color=="adjp"){
color <- V(g)$adjp[!is.na(ind)]
}else if(node.color=="zscore"){
color <- V(g)$zscore[!is.na(ind)]
}else if(node.color=="nOverlap"){
color <- V(g)$nOverlap[!is.na(ind)]
}
color[color<=zlim[1]] <- zlim[1]
color[color>=zlim[2]] <- zlim[2]
if(node.size=="or"){
size <- V(g)$or[!is.na(ind)]
}else if(node.size=="adjp"){
size <- V(g)$adjp[!is.na(ind)]
}else if(node.size=="zscore"){
size <- V(g)$zscore[!is.na(ind)]
}else if(node.size=="nOverlap"){
size <- V(g)$nOverlap[!is.na(ind)]
}
size[size<=slim[1]] <- slim[1]
size[size>=slim[2]] <- slim[2]
df <- data.frame(df_tips[ind[!is.na(ind)],], color=color, size=size, group=group, group_id=group_id, x_group=x_group, y_group=y_group, stringsAsFactors=F)
})
df <- do.call(rbind, ls_df)
# if multiple groups
if(length(ls_igg)>1){
## add polygon
gp <- gp + geom_polygon(data=df, aes(x=x*x_group, y=y*y_group, group=group, color=group),fill="transparent",size=group.size) + scale_colour_manual(values=xColormap(paste0(group.color,"-",group.color))(length(unique(df$group))), guide=guide_legend(title="Circles",keywidth=0.5,keyheight=0.6, order=1, nrow=min(20,length(unique(df$group)))))
## add polygon labelling
tipid <- NULL
gp <- gp + geom_text(data=subset(df,tipid==1), aes(x=x*x_group+0.1, y=y*y_group, label=group_id),color=group.label.color,size=group.label.size)
}
gp <- gp + geom_point(data=df, aes(x=x*x_group, y=y*y_group, fill=color, size=size), alpha=1, color=group.color, shape=21)
if(legend.direction=="auto"){
if(length(ls_igg)>1){
legend.direction <- "horizontal"
}else{
legend.direction <- "vertical"
}
}
if(legend.direction=="vertical"){
gp <- gp + scale_size_continuous(limits=slim, range=node.size.range, guide=guide_legend(node.size.title,title.position="top",ncol=1,order=2))
gp <- gp + scale_fill_gradientn(colors=xColormap(colormap)(64), limits=zlim, guide=guide_colorbar(title=node.color.title,title.position="top",barwidth=0.5,order=3))
}else if(legend.direction=="horizontal"){
gp <- gp + scale_size_continuous(limits=slim, range=node.size.range, guide=guide_legend(node.size.title,title.position="top",keywidth=0.5,keyheight=0.5,ncol=3,byrow=T,order=2))
gp <- gp + scale_fill_gradientn(colors=xColormap(colormap)(64), limits=zlim, guide=guide_colorbar(title=node.color.title,title.position="top",barheight=0.5,direction="horizontal",order=3))
}
gp$data_enrichment <- df
}
return(gp)
}
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Defines functions xEnrichCtree
Documented in xEnrichCtree
#' Function to visualise enrichment results using a tree-like circular plot
#'
#' \code{xEnrichCtree} is supposed to visualise enrichment results using a tree-like circular plot.
#'
#' @param eTerm an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having all these columns ('name','adjp','or','zscore','nOverlap'; 'group' optionally)
#' @param ig an object of class "igraph" with node attribute 'name'. It could be a 'phylo' object converted to. Note: the leave labels would be the node attribute 'name' unless the node attribute 'label' is explicitely provided
#' @param FDR.cutoff FDR cutoff used to show the significant terms only. By default, it is set to NULL; useful when nodes sized by FDR
#' @param node.color which statistics will be used for node coloring. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score
#' @param colormap short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in \url{http://html-color-codes.info/color-names}
#' @param zlim the minimum and maximum values for which colors should be plotted
#' @param node.size which statistics will be used for node size. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score
#' @param slim the minimum and maximum values for which sizes should be plotted
#' @param node.size.range the range of actual node size
#' @param group.gap the gap between group circles. Only works when multiple groups provided
#' @param group.color the color of group circles. Only works when multiple groups provided
#' @param group.size the line width of group circles. Only works when multiple groups provided
#' @param group.label.size the size of group circle labelling. Always a sequential integer located at the top middle. Only works when multiple groups provided
#' @param group.label.color the color of group circle labelling. Only works when multiple groups provided
#' @param legend.direction the legend guide direction. It can be "horizontal" (useful for many groups with lengthy labelling), "vertical" and "auto" ("vertical" when multiple groups provided; otherwise "horizontal")
#' @param leave.label.orientation the leave label orientation. It can be "outwards" and "inwards"
#' @param ... additional graphic parameters used in xCtree
#' @return
#' a ggplot2 object appended with 'ig', 'data' which should contain columns 'x','y', 'leaf' (T/F), 'name' (the same as V(ig)$name), 'tipid' (tip id), 'label' (if not given in ig, a 'name' varient), 'angle' and 'hjust' (assist in leave label orientation), and 'data_enrichment' (enrichment results for tips)
#' @note none
#' @export
#' @seealso \code{\link{xCtree}}
#' @include xEnrichCtree.r
#' @examples
#' \dontrun{
#' # Load the XGR package and specify the location of built-in data
#' library(XGR)
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
#'
#' # load the atlas of AA pathways
#' AA.template <- xRDataLoader("AA.template", RData.location=RData.location)
#' # consensus tree
#' ig <- AA.template$consensus$ig
#'
#' # enrichment analysis using AA pathways
#' input <- xRDataLoader('Haploid_regulators_all', RData.location=RData.location)
#' data <- subset(input, Phenotype=="AKT")
#' genes <- data$Gene[data$FDR<0.05]
#' background <- data$Gene
#' eTerm <- xEnricherGenes(genes, background=background, ontology="AA", min.overlap=5, test="fisher", RData.location=RData.location)
#'
#' # circular visualisation of enriched AA pathways
#' gp <- xEnrichCtree(eTerm, ig)
#'
#' ###############################
#' # advanced use: multiple groups
#' # enrichment analysis using AA pathways
#' Haploid <- subset(input, FDR<0.05)
#' ls_group <- split(x=Haploid$Gene, f=Haploid$Phenotype)
#' background <- unique(input$Gene)
#' ls_eTerm <- xEnricherGenesAdv(ls_group, background=background, ontologies="AA", test="fisher", min.overlap=5, RData.location=RData.location)
#'
#' # circular visualisation of enriched AA pathways
#' gp <- xEnrichCtree(ls_eTerm, ig)
#' }
xEnrichCtree <- function(eTerm, ig, FDR.cutoff=NULL, node.color=c("zscore","adjp","or","nOverlap"), colormap="brewer.Reds", zlim=NULL, node.size=c("adjp","zscore","or","nOverlap"), slim=NULL, node.size.range=c(0.5,4.5), group.gap=0.08, group.color="lightblue", group.size=0.2, group.label.size=2, group.label.color="black", legend.direction=c("auto","horizontal","vertical"), leave.label.orientation=c('inwards','outwards'), ...)
{
## match.arg matches arg against a table of candidate values as specified by choices, where NULL means to take the first one
node.color <- match.arg(node.color)
node.size <- match.arg(node.size)
legend.direction <- match.arg(legend.direction)
leave.label.orientation <- match.arg(leave.label.orientation)
if(is.null(eTerm)){
warnings("There is no enrichment in the 'eTerm' object.\n")
return(NULL)
}
if(class(ig)!="igraph"){
warnings("The 'ig' object must be provided.\n")
return(NULL)
}else{
if(!("name" %in% igraph::vertex_attr_names(ig))){
warnings("The 'ig' object must contain a node attribute 'name'.\n")
return(NULL)
}
}
if(class(eTerm)=='eTerm'){
df_enrichment_group <- xEnrichViewer(eTerm, top_num="all")
df_enrichment_group$group <- 'group'
}else if(class(eTerm)=='ls_eTerm' | class(eTerm)=='data.frame'){
if(class(eTerm)=='ls_eTerm'){
df_enrichment_group <- eTerm$df
}else if(class(eTerm)=='data.frame'){
if(all(c('group','name','adjp','or','zscore','nOverlap') %in% colnames(eTerm))){
df_enrichment_group <- eTerm[,c('group','name','adjp','or','zscore','nOverlap')]
}else if(all(c('name','adjp','or','zscore','nOverlap') %in% colnames(eTerm))){
df_enrichment_group <- eTerm[,c('name','adjp','or','zscore','nOverlap')]
df_enrichment_group$group <- 'group'
}
}
}
##########
# force those insignificant (FDR) to 1; useful when nodes sized by FDR
if(!is.null(FDR.cutoff)){
df_enrichment_group$adjp[df_enrichment_group$adjp>=FDR.cutoff] <- 1
}
##########
if(class(df_enrichment_group$group)=='factor'){
if(length(unique(df_enrichment_group$group)) != length(levels(df_enrichment_group$group))){
df_enrichment_group$group <- factor(df_enrichment_group$group, levels=sort(unique(df_enrichment_group$group)))
}
}
gp <- NULL
if(class(ig)=="igraph"){
#########################
## replace those infinite
df_enrichment_group$or[is.infinite(df_enrichment_group$or)] <- max(df_enrichment_group$or[!is.infinite(df_enrichment_group$or)])
#########################
# convert 'ig' into 'ls_igg' by group
ls_df <- split(x=df_enrichment_group[,c("name","zscore","adjp","or","nOverlap")], f=df_enrichment_group$group)
ls_igg <- lapply(ls_df, function(df_enrichment){
igg <- ig
V(igg)$zscore <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$zscore[!is.na(ind)] <- df_enrichment$zscore[ind[!is.na(ind)]]
V(igg)$adjp <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$adjp[!is.na(ind)] <- -1*log10(df_enrichment$adjp)[ind[!is.na(ind)]]
V(igg)$or <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$or[!is.na(ind)] <- log2(df_enrichment$or)[ind[!is.na(ind)]]
V(igg)$nOverlap <- 0
ind <- match(V(igg)$name, df_enrichment$name)
V(igg)$nOverlap[!is.na(ind)] <- df_enrichment$nOverlap[ind[!is.na(ind)]]
igg
})
if(node.color=="or"){
node.color.title <- expression(log[2](OR))
if(is.null(zlim)){
zlim <- c(0, ceiling(max(log2(df_enrichment_group$or))))
}
}else if(node.color=="adjp"){
node.color.title <- expression(-log[10](FDR))
if(is.null(zlim)){
zlim <- c(0, ceiling(max(-1*log10(df_enrichment_group$adjp))))
}
}else if(node.color=="zscore"){
node.color.title <- "Z-score"
if(is.null(zlim)){
zlim <- c(0, ceiling(max(df_enrichment_group$zscore)))
}
}else if(node.color=="nOverlap"){
node.color.title <- "# genes"
if(is.null(zlim)){
zlim <- c(0, ceiling(max(df_enrichment_group$nOverlap)))
}
}
if(node.size=="or"){
node.size.title <- expression(log[2](OR))
if(is.null(slim)){
slim <- c(0, ceiling(max(log2(df_enrichment_group$or))))
}
}else if(node.size=="adjp"){
node.size.title <- expression(-log[10](FDR))
if(is.null(slim)){
slim <- c(0, ceiling(max(-1*log10(df_enrichment_group$adjp))))
}
}else if(node.size=="zscore"){
node.size.title <- "Z-score"
if(is.null(slim)){
slim <- c(0, ceiling(max(df_enrichment_group$zscore)))
}
}
else if(node.size=="nOverlap"){
node.size.title <- "Num of genes"
if(is.null(slim)){
slim <- c(0, ceiling(max(df_enrichment_group$nOverlap)))
}
}
x <- y <- leaf <- x_group <- y_group <- group <- group_id <- color <- size <- NULL
if(length(ls_igg)>1){
leave.label.orientation <- 'inwards'
}
gp <- xCtree(ig, leave.label.orientation=leave.label.orientation, ...)
df_tips <- subset(gp$data, leaf==T)
ls_df <- lapply(1:length(ls_igg), function(i){
g <- ls_igg[[i]]
if(length(ls_igg)<10){
# 0-leading
group <- paste0(i, ": ", names(ls_igg)[i])
group_id <- i
}else{
group <- sprintf("%02d: %s", i, names(ls_igg)[i])
group_id <- sprintf("%02d", i)
}
x_group <- 1.05+(i-1)*group.gap
y_group <- 1.05+(i-1)*group.gap
ind <- match(V(g)$name, df_tips$name)
if(node.color=="or"){
color <- V(g)$or[!is.na(ind)]
}else if(node.color=="adjp"){
color <- V(g)$adjp[!is.na(ind)]
}else if(node.color=="zscore"){
color <- V(g)$zscore[!is.na(ind)]
}else if(node.color=="nOverlap"){
color <- V(g)$nOverlap[!is.na(ind)]
}
color[color<=zlim[1]] <- zlim[1]
color[color>=zlim[2]] <- zlim[2]
if(node.size=="or"){
size <- V(g)$or[!is.na(ind)]
}else if(node.size=="adjp"){
size <- V(g)$adjp[!is.na(ind)]
}else if(node.size=="zscore"){
size <- V(g)$zscore[!is.na(ind)]
}else if(node.size=="nOverlap"){
size <- V(g)$nOverlap[!is.na(ind)]
}
size[size<=slim[1]] <- slim[1]
size[size>=slim[2]] <- slim[2]
df <- data.frame(df_tips[ind[!is.na(ind)],], color=color, size=size, group=group, group_id=group_id, x_group=x_group, y_group=y_group, stringsAsFactors=F)
})
df <- do.call(rbind, ls_df)
# if multiple groups
if(length(ls_igg)>1){
## add polygon
gp <- gp + geom_polygon(data=df, aes(x=x*x_group, y=y*y_group, group=group, color=group),fill="transparent",size=group.size) + scale_colour_manual(values=xColormap(paste0(group.color,"-",group.color))(length(unique(df$group))), guide=guide_legend(title="Circles",keywidth=0.5,keyheight=0.6, order=1, nrow=min(20,length(unique(df$group)))))
## add polygon labelling
tipid <- NULL
gp <- gp + geom_text(data=subset(df,tipid==1), aes(x=x*x_group+0.1, y=y*y_group, label=group_id),color=group.label.color,size=group.label.size)
}
gp <- gp + geom_point(data=df, aes(x=x*x_group, y=y*y_group, fill=color, size=size), alpha=1, color=group.color, shape=21)
if(legend.direction=="auto"){
if(length(ls_igg)>1){
legend.direction <- "horizontal"
}else{
legend.direction <- "vertical"
}
}
if(legend.direction=="vertical"){
gp <- gp + scale_size_continuous(limits=slim, range=node.size.range, guide=guide_legend(node.size.title,title.position="top",ncol=1,order=2))
gp <- gp + scale_fill_gradientn(colors=xColormap(colormap)(64), limits=zlim, guide=guide_colorbar(title=node.color.title,title.position="top",barwidth=0.5,order=3))
}else if(legend.direction=="horizontal"){
gp <- gp + scale_size_continuous(limits=slim, range=node.size.range, guide=guide_legend(node.size.title,title.position="top",keywidth=0.5,keyheight=0.5,ncol=3,byrow=T,order=2))
gp <- gp + scale_fill_gradientn(colors=xColormap(colormap)(64), limits=zlim, guide=guide_colorbar(title=node.color.title,title.position="top",barheight=0.5,direction="horizontal",order=3))
}
gp$data_enrichment <- df
}
return(gp)
}
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