Tool: chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
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gravatar for lakshayanand15
15 months ago by
United States
lakshayanand1540 wrote:

chromoMap is an R package that can be used to create interactive visualizations and annotation of entire chromosomes or chromosome regions of any living organism. It takes BED like files to specify the coordinates of the chromosomes and the annotations separately.chromosomes are rendered as a continuous composition of loci where you can hover on a locus to see detailed annotation for the genomic range of that locus. It is available on CRAN( version 0.2 ). It provides many features like:

  • visualize different sets of chromosomes(polyploidy) on the same plot that can be used for cross-species or multi-sample comparisons.
  • associate numeric data and create chromosome heatmaps or visualize group annotations
  • add hyperlinks to your favorite database and many more like add labelings, change colors and embellish your plots.

You can explore more at my blog or reading my publication preprint (for more research insights). read vignette for function documentation.enter link description here example static snapshot:enter image description here or see live interactive example here.

ADD COMMENTlink written 15 months ago by lakshayanand1540

I prepared a chromosome file (c_plot) as

NC_037545.1     1       202105980
NC_037546.1     1       188952477
NC_037547.1     1       175630833

Annotation file (de_lncrna.annotation) as:

LOC112581744    NC_037545.1     6566415 6567888
LOC112582356    NC_037545.1     8234378 8238149
LOC112582960    NC_037545.1     12240957        12245030

I did

annot_dat <- read.table(file = "~/lncrna/chromomap/de_lncrna.annotation", sep="\t", quote="", stringsAsFactors=FALSE)
chrom_dat <- read.table(file = "~/lncrna/chromomap/c_plot", sep="\t", quote="", stringsAsFactors=FALSE)

> chromoMap(chrom_dat, annot_dat)
**Error**: The number of data files(s) must same as the number of chromsome file(s)
**Error** in chromoMap(chrom_dat, annot_dat) :

I have one chromosome and one annotation file only, I specified it as per manual, but I am getting this error.

Kindly help!

ADD REPLYlink modified 22 days ago • written 22 days ago by kousi3110

Hello,

chromoMap() takes the file-names directly as input. Try passing the filenames directly as:

chromoMap( "~/lncrna/chromomap/c_plot", "~/lncrna/chromomap/de_lncrna.annotation")

or you could save the names in character variable: annot_dat <- "~/lncrna/chromomap/de_lncrna.annotation" chrom_dat <- "~/lncrna/chromomap/c_plot"

and then do, chromoMap(chrom_dat, annot_dat)

I hope that is helpful.

Thank you for trying chromoMap. Cheers, Lakshay

ADD REPLYlink written 21 days ago by lakshayanand1540
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