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Question: Multiple samples on the same graph
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gravatar for Luiz
5 days ago by
Luiz0
Brazil
Luiz0 wrote:

Hi, good morning!

I hope you have a nice weekend.

I'm working on pathview today and i can't put different matrixes on the graph to compare. Only one is working and my version is 1.14.0. Already run the demo code and everything is fine accord with vignette.

I'm trying to do this : https://bioconductor.org/packages/devel/bioc/vignettes/pathview/inst/doc/pathview.pdf pg14

Workflow

setwd("~/R")
require(dplyr)
require(DESeq2)
require(ggplot2)
require(ggrepel)
require(pheatmap)
library(pathview)
library(gage)
library(gageData)
data(kegg.sets.hs)
data(sigmet.idx.hs)
data(gse16873.d)

kegg.sets.hs = kegg.sets.hs[sigmet.idx.hs]
head(kegg.sets.hs, 3)
bckCountTable <- read.table("Matrix.txt", header=TRUE, row.names=1)
samples <- data.frame(row.names=c("R1", "R2", "R3","IR1","IR2", "IR3"), condition=as.factor(c(rep("R",3),rep("IR",3))))
samples
bckCDS <- DESeqDataSetFromMatrix(countData = bckCountTable, colData=samples, design=~condition)
bckCDS <- bckCDS[ rowSums(counts(bckCDS)) > 1, ]
bckCDS_1 <- DESeq(bckCDS)
res <- results(bckCDS_1, alpha=0.05, betaPrior = F, contrast=c("condition", "IR", "R"), pAdjustMethod = "BH")
res$symbol = mapIds(org.Hs.eg.db,
                    keys=row.names(res), 
                    column="SYMBOL",
                    keytype="REFSEQ",
                    multiVals="first")
res$entrez = mapIds(org.Hs.eg.db,
                    keys=row.names(res), 
                    column="ENTREZID",
                    keytype="REFSEQ",
                    multiVals="first")
res$name = mapIds(org.Hs.eg.db,
                    keys=row.names(res), 
                    column="GENENAME",
                    keytype="REFSEQ",
                    multiVals="first")
foldchanges = res$log2FoldChange
names(foldchanges) = res$entrez
head(foldchanges)
head(res,10)
foldchanges = res$log2FoldChange
names(foldchanges) = res$entrez
head(foldchanges)
keggres = gage(foldchanges, gsets=kegg.sets.hs, same.dir=TRUE)
lapply(keggres, head)

bckCountTable2 <- read.table("Matrix2.txt", header=TRUE, row.names=1)
samples2 <- data.frame(row.names=c("CTL1", "CTL2", "CTL3","HT1","HT2", "HT3"), condition=as.factor(c(rep("CTL",3),rep("HT",3))))
samples2
bckCDS2 <- DESeqDataSetFromMatrix(countData = bckCountTable2, colData=samples2, design=~condition)
bckCDS2 <- bckCDS2[ rowSums(counts(bckCDS2)) > 1, ]
bckCDS_12 <- DESeq(bckCDS2)
res2 <- results(bckCDS_12, alpha=0.05, betaPrior = F, contrast=c("condition", "HT", "CTL"), pAdjustMethod = "BH")
res2$symbol = mapIds(org.Hs.eg.db,
                    keys=row.names(res2), 
                    column="SYMBOL",
                    keytype="REFSEQ",
                    multiVals="first")
res2$entrez = mapIds(org.Hs.eg.db,
                    keys=row.names(res2), 
                    column="ENTREZID",
                    keytype="REFSEQ",
                    multiVals="first")
res2$name = mapIds(org.Hs.eg.db,
                    keys=row.names(res2), 
                    column="GENENAME",
                    keytype="REFSEQ",
                    multiVals="first")
foldchanges2 = res2$log2FoldChange
names(foldchanges2) = res2$entrez
head(foldchanges2)
head(res2,10)
foldchanges2 = res2$log2FoldChange
names(foldchanges2) = res2$entrez
head(foldchanges2)
keggres2 = gage(foldchanges2, gsets=kegg.sets.hs, same.dir=TRUE)
lapply(keggres2, head)

Then i proceed to:

pv.out <- pathview(gene.data = foldchanges, cpd.data = foldchanges2, pathway.id = "any", + species = "hsa", out.suffix = "any", keys.align = "y", + kegg.native = T, match.data = F, multi.state = T, same.layer = T) 

But i get a graph with only the gene.data, like cpd.data don't exist.

Thank you for your attention!

 

ADD COMMENTlink modified 1 day ago by Michael Love12k • written 5 days ago by Luiz0
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