shinyPathview {GDCRNATools} | R Documentation |
A simple shiny app to show pathways genetrated by pathview package on local web browser
shinyPathview(gene, pathways, directory = ".")
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 |
a local webpage for visualization of KEGG maps
Ruidong Li and Han Qu
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)