plot_pathway_overall: plot_pathway_overall

In KEGGprofile: An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway

Description

The function will plot the correlation distributions for each enriched pathway (result from find_enriched_pathway function), and then Wilcoxon tests would be used to estimate the significance of values distribution between genes in each pathway and all other genes.

Usage

plot_pathway_overall(gene_values, species = "hsa",
  pathwayNumInFigure = 5, rankByVar = colnames(gene_values)[1])

Arguments

gene_values	A data.frame or matrix with gene ID as rownames. Each column represent gene value in one condition.
species	the species id in KEGG database, 'hsa' means human, 'mmu' means mouse, 'rno' means rat, etc
pathwayNumInFigure	a integer specifying max number of (top) pathways in each direction in the boxplot.
rankByVar	a character string specifying variable (sample) name by which to rank the boxplot.

Value

p values for Wilcoxon tests in each pathway

Examples

data(pro_pho_expr)
data(pho_sites_count)
gene_values<-pro_pho_expr[row.names(pho_sites_count)[which(pho_sites_count>=10)],]
plot_pathway_overall(gene_values=gene_values[,1:3])

KEGGprofile documentation built on Nov. 8, 2020, 6:13 p.m.