plot_pathway_cor: plot_pathway_cor

In slzhao/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 correlations distribution between genes in each pathway and all genes.

Usage

plot_pathway_cor(gene_expr, kegg_enriched_pathway, groups = NULL,
  side = c("both", "pos", "neg"), alternative = NULL)

Arguments

gene_expr	the matrix for gene expression, row.names should be NCBI gene ID, such as 67040, 93683
kegg_enriched_pathway	The returned value from find_enriched_pathway function, the enriched pathways.
groups	a character used to indicate expression values from different types of samples
side	a character string specifying the correlation directions interested, must be one of "both" (default), "pos" or "neg".
alternative	a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less". You can specify just the initial letter.

Value

p values for Wilcoxon tests in each pathway

Examples

data(pro_pho_expr)
data(pho_sites_count)
genes<-row.names(pho_sites_count)[which(pho_sites_count>=10)]
pho_KEGGresult<-find_enriched_pathway(genes,species='hsa')
result<-plot_pathway_cor(gene_expr=pro_pho_expr,kegg_enriched_pathway=pho_KEGGresult)

slzhao/KEGGprofile documentation built on Oct. 27, 2020, 4:29 a.m.