[genoPlotR-help] genoPlotR custom colour dna_seg

[Lionel Guy]

Mmh... The crux lies in the read.table function (called by 
read_dna_seg_from_tab) interpreting the "#" as comments, and there is no 
simple way to change that with the current code. I will fix that in a 
future release, but my time is scarce, so who knows when that's going to 
happen.

As a decent workaround, you can code your colors in hex, including the # 
in front of the color, load your file with read.table, turning the 
comment recognition off, and then turn it into a dna_seg object:

df <- read.table(file="testHexColors.dna_seg", header=TRUE, comment="", 
stringsAsFactors=FALSE)
A_aspergillus_nad5 <- as.dna_seg(df)
plot_gene_map(dna_segs= list(A_aspergillus_nad5,A_aspergillus_nad5), 
dna_seg_labels= c("A_aspergillus", "A_aspergillus"));

HTH,

Lionel

On 03/25/2015 02:37 PM, Alejandro Manzano Marin wrote:
> Hey ive tried giving both hex colours directly with and without
> quotations marks and with the rgb function but no luck at least not
> reading it directly with the read_dna_seg_from_tab function. I attach
> you my input file with the colours as names, what i did was just change
> the colour anme white for hex or rgb to get the errors
>
> CODE
> A_aspergillus_nad5 <-
> read_dna_seg_from_tab(file="A_aspergillus_nad5.dna_seg", header=TRUE);
> plot_gene_map(dna_segs= list(A_aspergillus_nad5,A_aspergillus_nad5),
> dna_seg_labels= c("A_aspergillus", "A_aspergillus"));
>
> ERRORS
> # rgb colour
> Error in grid.Call.graphics(L_polygon, x$x, x$y,
> list(as.integer(seq_along(x$x)))) :
>    invalid color name 'rgb(255, 103, 181, 255, maxColorValue=255)'
> Calls: plot_gene_map ... drawDetails -> drawDetails.polygon ->
> grid.Call.graphics
> Execution halted
>
> # hex colour
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
> na.strings,  :
>    line 1 did not have 10 elements
> Calls: setColour_dna_seg ... nrow -> read_dna_seg_from_tab -> read.table
> -> scan
> Execution halted
>
>
> thanks for your help
>
>
> On 25/03/15 13:43, Lionel Guy wrote:
>> Hi Alejandro,
>>
>> Although I might not have tested it, I thought giving hex or rgb
>> colors in the dna_seg file should work. Could you please send me the
>> errors that you get, as well as (a subset of) your input file?
>>
>> Best regards,
>>
>> Lionel
>>
>>> On 25 Mar 2015, at 12:31 , Alejandro Manzano Marin
>>> <alejandro.manzano at uv.es> wrote:
>>>
>>> hi, i was wondering how could i either define a custom colour name in
>>> R to be able to ame it direcly in my dna_seg file or is there a way
>>> to give rgb or hex colkours in the dna_seg file instead of colour
>>> names. I have tried putting directly the hex colour and rgb() but get
>>> errors, i guess because it expects the colours to be string of names
>>> for colours.
>>>
>>> thanks
>>>
>>> --
>>> Alejandro Manzano Marín
>>> Genomic Sciences Graduate
>>> Universidad Nacional Autónoma de México (UNAM)
>>> amanzano at lcg.unam.mx
>>> M.Sc. Molecular, Cell Biology and Genetics
>>> Institut Cavanilles de Biodiversitat i Biologia Evolutiva
>>> Department of Evolutionary Genetics
>>> C/ Catedrático José Beltrán nº 2
>>> 46980 Paterna, València, España
>>> Phone: (+34)963-543-651
>>> Fax: (+34)963-543-670
>>> alejandro.manzano at uv.es
>>>
>>>
>>
>
>