R/xEnrichForest.r

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

#' Function to visualise enrichment results using a forest plot
#'
#' \code{xEnrichForest} is supposed to visualise enrichment results using a forest plot. A point is colored by the significance level, and a horizontal line for the 95% confidence interval (CI) of odds ratio (OR; the wider the CI, the less reliable). It returns an object of class "ggplot".
#'
#' @param eTerm an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having all these columns (named as 'group','ontology','name','adjp','or','CIl','CIu')
#' @param top_num the number of the top terms (sorted according to OR). For the eTerm object, if it is 'auto' (for eTerm), only the significant terms (see below FDR.cutoff) will be displayed
#' @param FDR.cutoff FDR cutoff used to declare the significant terms. By default, it is set to 0.05. Only works when top_num is 'auto' above
#' @param CI.one logical to indicate whether to allow the inclusion of one in CI. By default, it is TURE (allowed)
#' @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 values for which colors should be plotted, defaulting to the range of the -log10(FDR)
#' @param barwidth the width of the colorbar. Default value is 'legend.key.width' or 'legend.key.size' in 'theme' or theme
#' @param barheight the height of the colorbar. Default value is 'legend.key.height' or 'legend.key.size' in 'theme' or theme
#' @param wrap.width a positive integer specifying wrap width of name
#' @param font.family the font family for texts
#' @param signature logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE showing which function is used to draw this graph
#' @param drop logical to indicate whether all factor levels not used in the data will automatically be dropped. If FALSE (by default), all factor levels will be shown, regardless of whether or not they appear in the data
#' @param sortBy which statistics will be used for sorting and viewing gene sets (terms). It can be "adjp" or "fdr" for adjusted p value (FDR), "pvalue" for p value, "zscore" for enrichment z-score, "fc" for enrichment fold change, "nAnno" for the number of sets (terms), "nOverlap" for the number in overlaps, "or" for the odds ratio, and "none" for ordering according to ID of terms. It only works when the input is an eTerm object
#' @return an object of class "ggplot"
#' @note none
#' @export
#' @seealso \code{\link{xEnricherGenes}}, \code{\link{xEnricherSNPs}}, \code{\link{xEnrichViewer}}
#' @include xEnrichForest.r
#' @examples
#' \dontrun{
#' # Load the library
#' library(XGR)
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"
#' 
#' # provide the input Genes of interest (eg 100 randomly chosen human genes)
#' ## load human genes
#' org.Hs.eg <- xRDataLoader(RData='org.Hs.eg', RData.location=RData.location)
#' set.seed(825)
#' data <- as.character(sample(org.Hs.eg$gene_info$Symbol, 100))
#' data
#' 
#' # optionally, provide the test background (if not provided, all human genes)
#' #background <- as.character(org.Hs.eg$gene_info$Symbol)
#' 
#' # 1) Gene-based enrichment analysis using REACTOME pathways
#' # perform enrichment analysis
#' eTerm <- xEnricherGenes(data, ontology="REACTOME", RData.location=RData.location)
#' ## forest plot of enrichment results
#' gp <- xEnrichForest(eTerm, top_num="auto", FDR.cutoff=0.05)
#' 
#' # 2) Gene-based enrichment analysis using ontologies (REACTOME and GOMF)
#' # perform enrichment analysis
#' ls_eTerm <- xEnricherGenesAdv(data, ontologies=c("REACTOME","GOMF"), RData.location=RData.location)
#' ## forest plot of enrichment results
#' gp <- xEnrichForest(ls_eTerm, FDR.cutoff=0.1)
#' }

xEnrichForest <- function(eTerm, top_num=10, FDR.cutoff=0.05, CI.one=T, colormap="ggplot2.top", ncolors=64, zlim=NULL, barwidth=0.5, barheight=NULL, wrap.width=NULL, font.family="sans", signature=FALSE, drop=F, sortBy=c("or","adjp","fdr","pvalue","zscore","fc","nAnno","nOverlap","none"))
{
    
    sortBy <- match.arg(sortBy)
    
    if(is.null(eTerm)){
        warnings("There is no enrichment in the 'eTerm' object.\n")
        return(NULL)
    }
    
    if(any(class(eTerm) %in% 'eTerm')){
		## when 'auto', will keep the significant terms
		df <- xEnrichViewer(eTerm, top_num="all")
		
		############
		if(!CI.one){
			ind <- which(df$CIl>1 | df$CIu<1)
			df <- df[ind,]
		}
		############
		
		if(top_num=='auto'){
			top_num <- sum(df$adjp<FDR.cutoff)
			if(top_num <= 1){
				warnings("There is no enrichment in the 'eTerm' object.\n")
				top_num <- 10
				message(sprintf("0 or 1 term found; instead the top %d terms sorted by '%s' are shown!", top_num, sortBy), appendLF=TRUE)
			}
		}
		df <- xEnrichViewer(eTerm, top_num=top_num, sortBy=sortBy)
		df$group <- 'group'
		df$ontology <- 'ontology'
		
	}else if(any(class(eTerm) %in% 'ls_eTerm') | any(class(eTerm) %in% c('data.frame','tbl_df','tbl'))){
	
		if(any(class(eTerm) %in% 'ls_eTerm')){
			## when 'auto', will keep the significant terms
			df <- eTerm$df
			
		}else if(any(class(eTerm) %in% c('data.frame','tbl_df','tbl'))){
			eTerm <- as.data.frame(eTerm)
			
			if(all(c('group','ontology','name','adjp','or','CIl','CIu') %in% colnames(eTerm))){
				df <- eTerm[,c('group','ontology','name','adjp','or','CIl','CIu')]
			
			}else if(all(c('group','name','adjp','or','CIl','CIu') %in% colnames(eTerm))){
				df <- eTerm[,c('group','name','adjp','or','CIl','CIu')]
				df$ontology <- 'ontology'
			
			}else if(all(c('ontology','name','adjp','or','CIl','CIu') %in% colnames(eTerm))){
				df <- eTerm[,c('ontology','name','adjp','or','CIl','CIu')]
				df$group <- 'group'
			
			}else if(all(c('name','adjp','or','CIl','CIu') %in% colnames(eTerm))){
				df <- eTerm[,c('name','adjp','or','CIl','CIu')]
				df$group <- 'group'
				df$ontology <- 'ontology'
			
			}else{
				warnings("The input data.frame does not contain required columns: c('group','ontology','name','adjp','or','CIl','CIu').\n")
				return(NULL)
			}
			
		}
		
		## columns are ordered as indicated by inputs
		df$group <- factor(df$group, levels=unique(df$group))
		
		############
		if(!CI.one){
			ind <- which(df$CIl>1 | df$CIu<1)
			df <- df[ind,]
		}
		############
		
		or <- group <- ontology <- rank <- adjp <- NULL
		df <- df %>% dplyr::arrange(-or)
		if(top_num=='auto'){
			df <- subset(df, df$adjp<FDR.cutoff)
		}else{
			top_num <- as.integer(top_num)
			df <- as.data.frame(df %>% dplyr::group_by(group,ontology) %>% dplyr::group_by(rank=rank(-or),add=TRUE) %>% dplyr::filter(rank<=top_num & adjp<FDR.cutoff))
		}
		
	}

	##########################
	##########################
	if(nrow(df)==0){
		return(NULL)
	}
	##########################
	##########################

	## text wrap
	if(!is.null(wrap.width)){
		width <- as.integer(wrap.width)
		res_list <- lapply(df$name, function(x){
			x <- gsub('_', ' ', x)
			y <- strwrap(x, width=width)
			if(length(y)>1){
				paste0(y[1], '...')
			}else{
				y
			}
		})
		df$name <- unlist(res_list)
	}
	
	name <- fdr <- or <- CIl <- CIu <- NULL
	group <- ontology <- NULL
	
	df$fdr <- -log10(df$adjp)
	if(is.null(zlim)){
		tmp <- df$fdr
		zlim <- c(floor(min(tmp)), ceiling(max(tmp[!is.infinite(tmp)])))
	}
	df$fdr[df$fdr<=zlim[1]] <- zlim[1]
	df$fdr[df$fdr>=zlim[2]] <- zlim[2]
	
	## order by 'or', 'adjp'
	if(class(eTerm)=='eTerm' & sortBy!='or'){
		df <- df[rev(1:nrow(df)),]
	}else{
		df <- df[with(df,order(group, ontology, or, -fdr)),]
	}
	df$name <- factor(df$name, levels=unique(df$name))

	###########################################
	bp <- ggplot(df, aes(x=name, y=log2(or), ymin=log2(CIl), ymax=log2(CIu), color=fdr))
	bp <- bp + geom_pointrange(size=0.3) + ylab(expression(log[2]("odds ratio")))
	bp <- bp + geom_hline(yintercept=0, color='black', linetype='dashed') + coord_flip()
	bp <- bp + theme_bw() + theme(legend.position="right",axis.title.y=element_blank(), axis.text.y=element_text(size=8,color="black"), axis.title.x=element_text(size=10,color="black"))
	bp <- bp + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
	bp <- bp + scale_colour_gradientn(colors=xColormap(colormap)(ncolors), limits=zlim, guide=guide_colorbar(title=expression(-log[10]("FDR")),title.position="top",barwidth=barwidth,barheight=barheight,draw.ulim=FALSE,draw.llim=FALSE))
	
	## caption
    if(signature){
    	caption <- paste("Created by xEnrichForest from XGR version", utils ::packageVersion("XGR"))
    	bp <- bp + labs(caption=caption) + theme(plot.caption=element_text(hjust=1,face='bold.italic',size=8,colour='#002147'))
    }
	
	## change font family to 'Arial'
	bp <- bp + theme(text=element_text(family=font.family))
	
	## put arrows on x-axis
	bp <- bp + theme(axis.line.x=element_line(arrow=arrow(angle=30,length=unit(0.25,"cm"), type="open")))
	
	## x-axis (actually y-axis) position
	#bp <- bp + scale_y_continuous(position="bottom")
	
	# facet_grid: partitions a plot into a matrix of panels
	## group (columns), ontology (rows)
	ngroup <- length(unique(df$group))
	nonto <- length(unique(df$ontology))
	if(ngroup!=1 | nonto!=1){
		scales <- "free_y"
		space <- "free_y"
		
		if(ngroup==1){
			bp <- bp + facet_grid(ontology~., scales=scales, space=space, drop=drop)
		}else if(nonto==1){
			bp <- bp + facet_grid(.~group, scales=scales, space=space, drop=drop)
		}else{
			bp <- bp + facet_grid(ontology~group, scales=scales, space=space, drop=drop)
		}
		
		## strip
		bp <- bp + theme(strip.background=element_rect(fill="transparent",color="transparent"), strip.text=element_text(size=8,face="bold.italic"))
	}
	
	invisible(bp)
}