I don't know anything about gene sequencing analysis. You may find better expertise for that on the Bioconductor mailing list.
On June 23, 2019 12:28:59 PM PDT, Yogesh Gupta <nabiyog...@gmail.com> wrote: >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, <jdnew...@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 <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. >> -- 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.