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 <nabiyogesh using 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 <nabiyogesh using 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]]
>
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