Question: clusterprofiler: Pathview and dotplot
gravatar for nsmaan
18 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 • 732 views
ADD COMMENTlink modified 18 months ago by Benn8.0k • written 18 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 18 months ago by Benn8.0k

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 18 months ago by Benn8.0k • written 18 months ago by nsmaan10
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