[R] How to allow duplicate names in R

[Yogesh Gupta]

Thanks Jeff

Actually these are Amplicon sequencing variant which are differ at single
nucleotide but may belongs to same genus, or further may be same species,
but may be different bacterial strain, so I will think about it what should
I do, may be I can plot with OTU ID and genus together...or can just
aggregate at genus level...could you please suggest how I can aggregate
same genus name ID while importing data into R.

Thanks
Yogesh

On Sun, 23 Jun 2019, 20:09 Jeff Newmiller, <jdnewmil using dcn.davis.ca.us> wrote:

> 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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> --
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>

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