[genoPlotR-help] genoplotR: setting up colors for dna segments based on name

[Lionel Guy]

Hi Migee,

There are various ways to do that. One is to have an extra "col" column 
in your tab file, giving colors for each gene. Color names have to be 
R-compatible, (e.g. look at colors() in R).

Otherwise, if you have a list of genes and a matching list if colors, 
you could do something like this:

## Just loading data, replacing names with bogus gene names
library(genoPlotR)
data(three_genes)
dna_segs[[1]]$name <- c("dnaA", "dnaA", "modB")
dna_segs[[2]]$name <- c("dnaA", "dnaC", "modD")
dna_segs[[3]]$name <- c("dnaC", "blaB", "modD")

## Creating a lookup table with gene names in one colum and colors in 
the second
lt <- data.frame(name=c("dnaA", "dnaC", "modB"),
                  col=c("red", "green", "yellow"),
                  stringsAsFactors=FALSE)

## Attributing colors to genes
for (i in 1:length(dna_segs)){
     dna_segs[[i]]$col <- "black"
     for (j in 1:nrow(lt)){
         dna_segs[[i]]$col[dna_segs[[i]]$name == lt$name[j]] <- lt$col[j]
     }
}

## Showing the result
annots <- list()
for (i in 1:length(dna_segs)){
     annots[[i]] <- auto_annotate(dna_segs[[i]], names=dna_segs[[i]]$name)
}
plot_gene_map(dna_segs, comparisons, annotations=annots)


If you still have problems, please send (part of) the data you have, it 
would help to solve it!

Cheers,

Lionel

On 03/06/2014 07:46 PM, Migun Shakya wrote:
> Hello,
>
> Is there a way to set the color of dna segments based on the name of the gene?
>
> I have set of genes with same name but from different genomes, i wanted to color the arrows based on its name.
> Right now when i read in my tab delimited file and convert it to dna_segs, it adds the default color blue.
>
>
>
> Thank you
>
> migee.
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