R/xEnrichNetplot.r

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

#' Function to visualise enrichment results using different network layouts
#'
#' \code{xEnrichNetplot} is supposed to visualise enrichment results using different network layouts. Also supported is to visualise the comparative enrichment results (see the function \code{\link{xEnrichCompare}})) with nodes/terms colored according to how many times being called significant. It returns an object of class 'igraph'.
#'
#' @param eTerm an object of class "eTerm" or an object "ggplot" (resulting from \code{\link{xEnrichCompare}})
#' @param top_num the number of the top terms (sorted according to FDR or adjusted p-values). If it is 'auto', only the significant terms (FDR < 0.05) will be displayed
#' @param displayBy which statistics will be used for displaying. It can be "fc" for enrichment fold change (by default), "adjp" or "fdr" for adjusted p value (or FDR), "pvalue" for p value, "zscore" for enrichment z-score
#' @param path.mode the mode of paths induced by nodes in query. It can be "all_paths" for all possible paths to the root, "shortest_paths" for only one path to the root (for each node in query), "all_shortest_paths" for all shortest paths to the root (i.e. for each node, find all shortest paths with the equal lengths)
#' @param node.info tells the ontology term information used to label nodes. It can be one of "none" for no node labeling, "term_id" for using Term ID, "term_name" for using Term Name, "both" for using both of Term ID and Name (the first 15 characters), and "full_term_name" for using the full Term Name
#' @param wrap.width a positive integer specifying wrap width of Term Name. By default, first 15 characters
#' @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), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "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 ncolors the number of colors specified over the colormap
#' @param zlim the minimum and maximum z/patttern values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted
#' @param colorbar logical to indicate whether to append a colorbar. If pattern is null, it always sets to false
#' @param newpage logical to indicate whether to open a new page. By default, it sets to true for opening a new page
#' @param glayout either a function or a numeric matrix configuring how the vertices will be placed on the plot. If layout is a function, this function will be called with the graph as the single parameter to determine the actual coordinates. This function can be one of "layout_nicely" (previously "layout.auto"), "layout_randomly" (previously "layout.random"), "layout_in_circle" (previously "layout.circle"), "layout_on_sphere" (previously "layout.sphere"), "layout_with_fr" (previously "layout.fruchterman.reingold"), "layout_with_kk" (previously "layout.kamada.kawai"), "layout_as_tree" (previously "layout.reingold.tilford"), "layout_with_lgl" (previously "layout.lgl"), "layout_with_graphopt" (previously "layout.graphopt"), "layout_with_sugiyama" (previously "layout.kamada.kawai"), "layout_with_dh" (previously "layout.davidson.harel"), "layout_with_drl" (previously "layout.drl"), "layout_with_gem" (previously "layout.gem"), "layout_with_mds". A full explanation of these layouts can be found in \url{http://igraph.org/r/doc/layout_nicely.html}
#' @param vertex.frame.color the color of the frame of the vertices. If it is NA, then there is no frame
#' @param vertex.size the size of each vertex. If it is a vector, each vertex may differ in size
#' @param vertex.color the fill color of the vertices. If it is NA, then there is no fill color. If the pattern is given, this setup will be ignored
#' @param vertex.shape the shape of each vertex. It can be one of "circle", "square", "csquare", "rectangle", "crectangle", "vrectangle", "pie" (\url{http://igraph.org/r/doc/vertex.shape.pie.html}), "sphere", and "none". If it sets to NULL, these vertices with negative will be "csquare" and the rest "circle". 
#' @param vertex.label the label of the vertices. If it is NA, then there is no label. The default vertex labels are the name attribute of the nodes
#' @param vertex.label.cex the font size of vertex labels.
#' @param vertex.label.dist the distance of the label from the center of the vertex. If it is 0 then the label is centered on the vertex. If it is 1 then the label is displayed beside the vertex.
#' @param vertex.label.color the color of vertex labels.
#' @param edge.arrow.size the size of the arrows for the directed edge. The default value is 1.
#' @param ... additional graphic parameters. See \url{http://igraph.org/r/doc/plot.common.html} for the complete list.
#' @return 
#' an igraph object to represent DAG, appended with a node attribute called 'enrichment'
#' @note none
#' @export
#' @seealso \code{\link{xEnricherGenes}}, \code{\link{xEnricherSNPs}}, \code{\link{xEnrichViewer}}
#' @include xEnrichNetplot.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/"
#' 
#' # 1) load eQTL mapping results: cis-eQTLs significantly induced by IFN
#' cis <- xRDataLoader(RData.customised='JKscience_TS2A', RData.location=RData.location)
#' ind <- which(cis$IFN_t > 0 & cis$IFN_fdr < 0.05)
#' df_cis <- cis[ind, c('variant','Symbol','IFN_t','IFN_fdr')]
#' data <- df_cis$variant
#' 
#' # 2) Enrichment analysis using Experimental Factor Ontology (EFO)
#' # Considering LD SNPs and respecting ontology tree
#' eTerm <- xEnricherSNPs(data, ontology="EF", include.LD="EUR", LD.r2=0.8, ontology.algorithm="lea", RData.location=RData.location)
#'
#' # 3) Net plot of enrichment results
#' subg <- xEnrichNetplot(eTerm, top_num="auto", displayBy="fc", node.info=c("none"), vertex.label=NA, wrap.width=30)
#' }

xEnrichNetplot <- function(eTerm, top_num=10, displayBy=c("fc","adjp","fdr","zscore","pvalue"), path.mode=c("all_paths","shortest_paths","all_shortest_paths"), node.info=c("none", "term_id", "term_name", "both", "full_term_name"), wrap.width=15, colormap=c("yr","jet","gbr","wyr","br","bwr","rainbow","wb"), ncolors=40, zlim=NULL, colorbar=T, newpage=T, glayout=layout_as_tree, vertex.frame.color=NA, vertex.size=NULL, vertex.color=NULL, vertex.shape=NULL, vertex.label=NULL, vertex.label.cex=NULL, vertex.label.dist=0.3, vertex.label.color="blue", edge.arrow.size=0.3, ...)
{
    
    displayBy <- match.arg(displayBy)
    path.mode <- match.arg(path.mode)
    node.info<- match.arg(node.info)
    
    if(is.logical(eTerm)){
        stop("There is no enrichment in the 'eTerm' object.\n")
    }
    
    if(class(eTerm)[1]=="eTerm"){
	
		## when 'auto', will keep the significant terms
		df <- xEnrichViewer(eTerm, top_num="all")
		if(top_num=='auto'){
			top_num <- sum(df$adjp<0.05)
			if(top_num<=1){
				top_num <- sum(df$adjp<0.1)
			}
			if(top_num <= 1){
				top_num <- 10
			}
		}
		df <- xEnrichViewer(eTerm, top_num=top_num, sortBy="adjp")
	
		g <- eTerm$g
		nodes_query <- rownames(df)
		subg <- dnet::dDAGinduce(g, nodes_query, path.mode=path.mode)
	
		## for data (pattern)
		if(displayBy=='adjp' | displayBy=='fdr'){
			data <- -1*log10(df$adjp)
		}else if(displayBy=='fc'){
			data <- df$fc
		}else if(displayBy=='pvalue'){
			data <- -1*log10(df$pvalue)
		}else if(displayBy=='zscore'){
			data <- df$zscore
		}
		names(data) <- rownames(df)
		ind <- match(V(subg)$name, names(data))
		data <- data[ind]
		names(data) <- V(subg)$name

	}else if(any(class(eTerm) %in% c("gg","ggplot"))){
		bp <- eTerm
		if(!is.null(bp$g)){
			bp_ig <- bp$g
			bp_data <- bp$data
			nodes_query <- unique(bp_data$id)
			subg <- dDAGinduce(g=bp_ig, nodes_query=nodes_query, path.mode=path.mode)
			data <- bp_data$nSig
			if(is.null(zlim)){
				zlim <- c(0, max(data))
			}
		}else{
			stop("No 'igraph' object can not be found in the input 'ggplot' object.\n")
		}
	}else{
		stop("Cannot find either an 'eTerm' object or an 'ggplot' object.\n")
	}
	
	
	## for vertex.label
    if(is.null(vertex.label)){
		## define node labels
		getTermInfo <- function(g, vids, numChar=15, mulLines=F){
			fullNames <- V(g)[vids]$term_name
			names(fullNames) <- V(g)[vids]$name
	
			if(mulLines==F){
				shortNames <- paste(substr(fullNames,1,numChar), ifelse(nchar(fullNames)>numChar, '...', ''), sep='')
			}else{
				shortNames <- sapply(fullNames,function(x){
					return(paste(strwrap(x, numChar), sep="", collapse = "\n"))
				})
			}
	
			names(shortNames) <- names(fullNames)
			return(shortNames)
		}
		termNames <- getTermInfo(subg, vids=V(subg)$term_id, numChar=15, mulLines=F)
		vertex.label <- switch(node.info,
						   none = NULL,
						   term_id = V(subg)$term_id,
						   term_name = V(subg)$term_name,
						   both = paste(V(subg)$term_id, termNames, sep="\n"),
						   full_term_name = getTermInfo(subg, vids=V(subg)$term_id, numChar=wrap.width, mulLines=T)
		)
    }
	
	######################################################################################
	## for data (pattern)
	pattern <- data
	
    if (!is.null(pattern)){
    
        flag <- 0
        if(!is.null(names(pattern))){
            pattern <- pattern[V(subg)$name]
        }
        if(length(pattern)==vcount(subg)){
            flag <- 1
        }
                
        if(flag==1){
        	
        	pattern <- as.numeric(pattern)
        	
        	pattern_nona <- pattern[!is.na(pattern)]
        	pattern_nona <- as.numeric(pattern_nona)
        	
            if(is.null(zlim)){
                vmin <- floor(stats::quantile(pattern_nona, 0.05))
                vmax <- ceiling(stats::quantile(pattern_nona, 0.95))
                if(vmin < 0 & vmax > 0){
                    vsym <- abs(min(vmin, vmax))
                    vmin <- -1*vsym
                    vmax <- vsym
                }
                zlim <- c(vmin,vmax)
            }
            
            ## A function to map a vector to colors
            vec2color <- function(vec, colormap=colormap, ncolors=ncolors, zlim=zlim){
                palette.name <- supraHex::visColormap(colormap=colormap)
                colors <- palette.name(ncolors)
                scale <- length(colors)/(max(zlim)-min(zlim))
                sapply(1:length(vec), function(x){
                	if(is.na(vec[x])){
                		'transparent'
                	}else{
						ind <- floor(1+(vec[x]-min(zlim))*scale)
						colors[max(1,min(ncolors,ind))]
					}
                })
            }
            vertex.color <- vec2color(pattern, colormap=colormap, ncolors=ncolors, zlim=zlim)
            vertex.frame.color <- vec2color(pattern, colormap=colormap, ncolors=ncolors, zlim=zlim)
            vertex.frame.color[vertex.frame.color=="transparent"] <- "grey"
        }else{
            warning("The input 'pattern' is ignored. Please check the help for enabling your input")
            pattern <- NULL
            if(is.null(vertex.color)){
                vertex.color <- "SkyBlue2"
            }
        }
    }else{
        if(is.null(vertex.color)){
            vertex.color <- "SkyBlue2"
        }
    }
    
    ######################################################################################
	
	########################################
	## append pattern data into igraph
	V(subg)$enrichment <- pattern
	########################################
	
	par_old <- graphics::par()
	
	dnet::visNet(g=subg, pattern=pattern, colormap=colormap, ncolors=ncolors, zlim=zlim, colorbar=colorbar, newpage=newpage, glayout=glayout, vertex.frame.color=vertex.frame.color, vertex.size=vertex.size, vertex.color=vertex.color, vertex.shape=vertex.shape, vertex.label=vertex.label, vertex.label.cex=vertex.label.cex, vertex.label.dist=vertex.label.dist, vertex.label.color=vertex.label.color, edge.arrow.size=edge.arrow.size, ...)
	
	suppressWarnings(graphics::par(par_old))
	
	invisible(subg)
}