Visualize genomic loci (overview)

Summary

We are using this R library.

https://cran.r-project.org/web/packages/chromoMap/vignettes/chromoMap.html

Input

  1. chrom size bed

chr1    0       249250621
chr2    0       243199373
chr3    0       198022430
chr4    0       191154276
chr5    0       180915260
chr6    0       171115067
chr7    0       159138663

  1. annotation bed

unique_label1 chr1 123456789 123456790 value_or_label unique_label2 chr2 start end value_or_label unique_label3 chr3 zz aa value_or_label unique_label4 chr4 cc dd value_or_label

The plot resolution is about 3MB per locus, so if two loci are less than 3MB distance, it will only plot one locus.

Usage

hpcf_interactive

module load conda3

source activate /home/yli11/.conda/r_env

to_chromoMap.R hg19_main.chrom_sizes.bed annot.bed

Output

chromoMAP_output.pdf and chromoMAP_output.html

Comments

code @ github.