shinyPathview: Shiny pathview

In Jialab-UCR/GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Description

A simple shiny app to show pathways genetrated by pathview package on local web browser

Usage

shinyPathview(gene, pathways, directory = ".")

Arguments

gene	a vector of numeric values (eg. fold change on log2 scale) with names are Ensembl gene ids
pathways	a vector of KEGG pathway ids
directory	the folder to save pathway figures. Default is the working directory

Value

a local webpage for visualization of KEGG maps

Author(s)

Ruidong Li and Han Qu

Examples

genes <- c('ENSG00000000938','ENSG00000000971','ENSG00000001036',
        'ENSG00000001084','ENSG00000001167','ENSG00000001460')
pathways <- c("hsa05414~Dilated cardiomyopathy (DCM)",
            "hsa05410~Hypertrophic cardiomyopathy (HCM)",
            "hsa05412~Arrhythmogenic right ventricular cardiomyopathy",
            "hsa04512~ECM-receptor interaction",
            "hsa04510~Focal adhesion",
            "hsa04360~Axon guidance",
            "hsa04270~Vascular smooth muscle contraction",
            "hsa05205~Proteoglycans in cancer",
            "hsa04022~cGMP-PKG signaling pathway",
            "hsa00480~Glutathione metabolism")
## Not run: shinyPathview(gene=genes, pathways=pathways)

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.