[BioC] Pathview plot split by experiment condition

[Luo Weijun]

If I understand you correctly you may try:

cnts.2cond=cbind(rowMeans(cnts.norm[ , samp.idx]),rowMeans(cnts.norm[ , ref.idx]))

then use cnts.2cond instead of cnts.d when calling pathview function:
pv.out.list <- sapply(path.ids2, function(pid) pathview(
                      gene.data = cnts.2cond, pathway.id = pid,
                      species = "hsa", out.suffix=out.suffix,
                      kegg.dir= "gageOutput/gageHG19", kegg.native=T, both.dirs = list(gene = F, cpd = T)))

Note this way, what are plotting the absolute expression not the expression changes, hence you need to set both.dirs = list(gene = F, cpd = T).
HTH,
Weijun

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On Fri, 5/23/14, Aric wrote:

 Weijun,

 I am not sure if
 what I want to do is possible, but I think it is. I would
 like to plot
 in pathview splitting by experiment condition for each gene
 instead of
 splitting by sample.

 For example, I have twelve samples divided equally into
 control and
 non-control. I would like to have one native kegg plot for
 each
 significant pathway, with the genes split according to
 whether the gene
 is up or down overall in the control or non-control group.
 It seemed
 like I have to use pure gage analysis to do this, but I can
 only get it
 split by sample.

 cnts.d <- cnts.norm[ , samp.idx] - rowMeans(cnts.norm[ ,
 ref.idx])
 path.ids <- c("hsa04670 Leukocyte transendothelial
 migration", "hsa04612 Antigen processing and presentation")
 path.ids2 <- substr(path.ids, 1, 8)
 pv.out.list <- sapply(path.ids2, function(pid) pathview(
                
       gene.data = cnts.d, pathway.id = pid,
                
       species = "hsa",
 out.suffix=out.suffix,
                
       kegg.dir= "gageOutput/gageHG19",
 kegg.native=T))

 If I replace 'gene.data = cnts.d' with 'cnts.d[, 1:2]' then
 I get
 splitting in the plot, but only between samples one and two.
 I would
 like it by experimental condition.

 Is this possible?