updated correlation plot functions to use module scores, average module expression (44eb9386) · Commits · github_fork / HdWGCNA

R/plotting.R

+35 −14

Original line number	Diff line number	Diff line
		@@ -34,17 +34,19 @@ PlotDendrogram <- function(
		)
		}

		#' MECorrelogram
		#' ModuleCorrelogram
		#'
		#' Plot Module Eigengene correlogram
		#'
		#' @param seurat_obj A Seurat object
		#' @param features What to plot? Can select hMEs, MEs, scores, or average
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		#' MECorrelogram
		MECorrelogram <- function(
		ModuleCorrelogram <- function(
		seurat_obj, wgcna_name = NULL, exclude_grey=TRUE,
		features = 'hMEs',
		type = 'upper', order='original', method='ellipse',
		tl.col = 'black', tl.srt=45,
		sig.level = c(0.0001, 0.001, 0.01, 0.05),
		@@ -54,8 +56,22 @@ MECorrelogram <- function(

		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

		# get MEs and convert to matrix
		MEs <- as.matrix(GetMEs(seurat_obj, wgcna_name))
		# get MEs, module data from seurat object
		if(features == 'hMEs'){
		MEs <- GetMEs(seurat_obj, TRUE, wgcna_name)
		} else if(features == 'MEs'){
		MEs <- GetMEs(seurat_obj, FALSE, wgcna_name)
		} else if(features == 'scores'){
		MEs <- GetModuleScores(seurat_obj, wgcna_name)
		} else if(features == 'average'){
		MEs <- GetAvgModuleExpr(seurat_obj, wgcna_name)
		restrict_range <- FALSE
		} else(
		stop('Invalid feature selection. Valid choices: hMEs, MEs, scores, average')
		)

		# convert to matrix
		MEs <- as.matrix(MEs)

		# exclude grey
		if(exclude_grey){
		@@ -97,6 +113,7 @@ MECorrelogram <- function(
		#' ModuleCorrNetwork
		ModuleCorrNetwork <- function(
		seurat_obj, wgcna_name=NULL, cluster_col=NULL, exclude_grey=TRUE,
		features = 'hMEs',
		reduction='umap', cor_cutoff=0.2, label_vertices=FALSE, edge_scale=5,
		vertex_size=15, niter=100, vertex_frame=FALSE
		){
		@@ -104,7 +121,20 @@ ModuleCorrNetwork <- function(
		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

		# Get module eigengenes
		MEs <- GetMEs(seurat_obj, wgcna_name)
		if(features == 'hMEs'){
		MEs <- GetMEs(seurat_obj, TRUE, wgcna_name)
		} else if(features == 'MEs'){
		MEs <- GetMEs(seurat_obj, FALSE, wgcna_name)
		} else if(features == 'scores'){
		MEs <- GetModuleScores(seurat_obj, wgcna_name)
		} else if(features == 'average'){
		MEs <- GetAvgModuleExpr(seurat_obj, wgcna_name)
		restrict_range <- FALSE
		} else(
		stop('Invalid feature selection. Valid choices: hMEs, MEs, scores, average')
		)

		# get modules
		modules <- GetModules(seurat_obj, wgcna_name)

		# exclude grey
		@@ -232,15 +262,6 @@ ModuleCorrNetwork <- function(
		vertex.label.cex=0.5,
		vertex.size=vertex_size
		)

		# plot colorbar:
		# TODO
		# Possibly get rid of this because it depends on a super random package
		# (fields) and kinda looks ugly?
		# colfunc <- colorRampPalette(c( "seagreen", "white", "darkorchid1"))
		# image.plot(legend.only=T, zlim=c(-1,1), col=colfunc(256) )
		#

		}

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