Pathway visualization¶
Summary¶
a good online server to search and visualize pathways containing a gene set
https://pathme.scai.fraunhofer.de/
Q: is there a way to highlight up and down-regulated genes in this visualization
A: PathView from R is able to do it (only for KEGG pathways). First, go to https://www.kegg.jp/ to find a list of KEGG pathway ids that contain your query gene, and then run pathview.R
source activate single_cell
library(pathview)
input_table = "20copy_vs_Jurkat.gene.final.combined.tpm.csv"
seperator = ","
LFC_column = "logFC"
if (seperator == "\\t"){
res <- read.csv(input_table, header=TRUE,sep="\t")
}else{
res <- read.csv(input_table, header=TRUE,sep=seperator)
}
rownames(res) = make.unique(as.character(res[,1]))
print (head(res))
pathway_ids = c("04060","04061","04144","04151","04630","04640","04658","04659","05162","05166","05200")
for (i in pathway_ids){
pv.out <- pathview(gene.data = res[LFC_column],
gene.idtype = "ENSEMBL",
pathway.id = i, species = "hsa", same.layer = T,
out.suffix = i, keys.align = "y", kegg.native = T,res=600,key.pos = "bottomright")
}