Question: clusterprofiler: Pathview and dotplot
gravatar for nsmaan
6 months ago by
nsmaan10 wrote:

Hello Experts. I have processed my RNA-seq data in a well-formatted text file (atleast i thought so..) that looks like this (~100+ genes) where i have Ensembl, entrezgene, gene(ID), group (up/down regulated), keggID, logFC, and padj, etc

> head(ids)
Ensembl entrezgene  gene    group   kegg    logFC   padj
ENSRNOG00000019500  24296   Cyp1a1  upregulated rno24296    2.441405    0.002797
ENSRNOG00000003280  24411   Grin2c  upregulated rno24411    6.245858    0.000071
ENSRNOG00000049590  24988   RT1-M2  downregulated   rno24988    -2.451328   0.000000
ENSRNOG00000014018  25280   St8sia1 downregulated   rno25280    -3.139369   0.000017
ENSRNOG00000001527  25408   Cd80    upregulated rno25408    2.669957    0.000050
ENSRNOG00000008157  29179   Syn2    upregulated rno29179    2.737939    0.001181
ENSRNOG00000011815  29517   Sgk1    downregulated   rno29517    -2.073134   0.000152

But no matter i much i try i can't get the Pathview and dotplot working on this file based on clusterprofiler documentation (which actually has excellent description, but i am limited by my basic R skills).

I would appreciate anyone's help in plotting Pathview and dotplot on a file like mine...

Thank you, -N

rna-seq • 316 views
ADD COMMENTlink modified 6 months ago by Benn7.5k • written 6 months ago by nsmaan10

If you show your code we can see where it goes wrong. Without any code it is impossible to diagnose.

ADD REPLYlink written 6 months ago by Benn7.5k

My input looks like this:

data<-read.delim("test.txt") # File is tab-delimited
#file contains columns of ENSEMBL, entrez, GENENAME, logFC, padj
genes<-data$entrez[abs(data$logFC)>1.5 & data$padj<0.01 ]
ego<- enrichGO(genes,OrgDb=,ont= "CC",  pAdjustMethod = "BH", pvalueCutoff  = 0.01,qvalueCutoff  = 0.05, readable= TRUE)
cnetplot(ego, categorySize="pvalue", foldChange=genes)
#barplot(ego, showCategory=8)

I can see cnetplot output but do not see the lines connecting cluster centers with genes?

Also i am not sure how to generate 'compareCluster' data to select up and downregulated groups (based on logFC and padj) for dotplot(formula_res) example provided in ....doc/clusterProfiler.html

I would appreciate any help in this... Thank you

ADD REPLYlink modified 6 months ago by Benn7.5k • written 6 months ago by nsmaan10
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