plot_pathway_overall {KEGGprofile} | R Documentation |
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.
plot_pathway_overall(gene_values, species = "hsa", pathwayNumInFigure = 5, rankByVar = colnames(gene_values)[1])
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. |
p values for Wilcoxon tests in each pathway
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])