Some concepts are so fundamental that they get encoded into general-purpose code. The idea that each row (column) of a heat map should be uniquely identifiable among all other rows (columns) is one such idea.
To break this rule you will have to create your own heatmap function. I strongly recommend that you not do this. Rather, you should study why there are duplicates in your data, and consider options such as removing duplicates, re-labelling duplicates, or aggregating the values corresponding to duplicates (e.g. mean, median, max...) before plotting so that the result will be meaningful to the viewer. On June 23, 2019 10:54:34 AM PDT, Yogesh Gupta <nabiyog...@gmail.com> wrote: >I able to do it with the below code but in heat map it shows x at >beginning >of each names. > > >x<-read.table("HEATMAP.ROOT.input.txt",sep="\t",head=T, >check.names=TRUE) > >x2 <- x[,-1] > >rownames(x2) <- make.names(x[,1], unique = TRUE) > >head(x2) > >> head(x2) > > Root_T1 Root_T2 Root_T3 > >X.GOUTA19 0.01179870 0.004254994 0.008371628 > >X.GOUTA19.1 0.01087136 0.025930026 0.012268479 > >X.Planctomyces 0.04665419 0.030925497 0.021187820 > >X.Methylomonas 0.01205195 0.019538770 0.035813232 > >X.Propionivibrio 0.10447746 0.286847806 0.184285575 > >X.Uliginosibacterium 0.16966278 0.193626963 0.232004759 > > > >How I can remove this X while plotting heat map: > >for heat map I am using pheatmap: > > >pheatmap(x2,scale="row",color =cm.colors(100),cluster_cols = >F,show_colnames = T,cluster_row=F,border_color="NA") > > >Thanks >Yogesh > > > > >On Sun, Jun 23, 2019 at 6:32 PM Yogesh Gupta <nabiyog...@gmail.com> >wrote: > >> Hi, >> >> I do have duplicates names in tab delimited files, I need to allow to >read >> these duplicate names in R, >> >> Could you please suggest how can modify this code to allow to read >> duplicates names: >> >> x<-read.table("HEATMAP.ROOT.input.txt",sep="\t",head=T, >check.names=FALSE) >> >> > x >> >> Genus Root_T1 Root_T2 Root_T3 >> >> 1 GOUTA19 0.011798697 0.004254994 0.008371628 >> >> 2 GOUTA19 0.010871359 0.025930026 0.012268479 >> >> 3 Planctomyces 0.046654187 0.030925497 0.021187820 >> >> 4 Methylomonas 0.012051952 0.019538770 0.035813232 >> >> 5 Propionivibrio 0.104477461 0.286847806 0.184285575 >> >> >> >> I need to make Genus name as row names but it shows error: >> >> >> x<-read.table("HEATMAP.ROOT.input.txt",sep="\t",head=T, >check.names=FALSE, >> row.names=1) >> >> *Error in read.table("HEATMAP.ROOT.input.txt", sep = "\t", head = T, >> check.names = FALSE, : * >> >> * duplicate 'row.names' are not allowed* >> >> >> *Kind Regards* >> >> *Yogesh* >> >> >> > > [[alternative HTML version deleted]] > >______________________________________________ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.