plot_heatmapsOnSel didn't work for dataset already annotated
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xubeisi • 0
@xubeisi-11767
Last seen 20 months ago
United States
 

 

library("MineICA")

dat <- data.frame(matrix(rnorm(10000),ncol=10,nrow=1000))
rownames(dat) <- paste("g", 1:1000, sep="")
colnames(dat) <- paste("s", 1:10, sep="")
## build a data.frame containing sample annotations
annot <- data.frame(type=c(rep("a",5),rep("b",5)))
rownames(annot) <- colnames(dat)
## run ICA
resJade <- runICA(X=dat, nbComp=3, method = "JADE")
## build params
params <- buildMineICAParams(resPath="toy/")
## build IcaSet object
icaSettoy <- buildIcaSet(params=params, A=data.frame(resJade$A), S=data.frame(resJade$S),
dat=dat, pData=annot, alreadyAnnot=TRUE)
params <- icaSettoy$params
icaSettoy <- icaSettoy$icaSet

keepvv = c("type")
keepcc <- 1

plot_heatmapsOnSel(icaSet = icaSettoy, selCutoff = 2, level = "genes", keepVar = keepvv, keepComp=keepcc, doSamplesDendro = TRUE, doGenesDendro = TRUE, heatmapCol = maPalette(low = "blue",high = "red", mid = "yellow", k=44), file = "heatmapWithDendro_zval3.pdf")

 

will report

 

Error in { : task 1 failed - "non-numeric matrix extent"
In addition: Warning message:
executing %dopar% sequentially: no parallel backend registered

 

if I change 

keepvv = c("type1")

the phenotype data won't draw but the heatmap seems fine. 

I tried several debug but still can't figure out how to make it work like using 

data(icaSetCarbayo)

 

Thanks!

 

 

MineICA • 749 views
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