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YaqiangCao / cLoops2

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
BSD 3-Clause "New" or "Revised" License
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how to plot loops #4

Closed ahmedabbas81 closed 2 years ago

ahmedabbas81 commented 2 years ago

Hello,

I am trying to plot loops in a bedpe file.

I understand I should use the function plot.plotLoops

However, can you please give me an example on the parameter loops in the function. Is it a dataframe? Can you please point me to an example using this function with its available data?

Thanks

YaqiangCao commented 2 years ago

Hello,

I am trying to plot loops in a bedpe file.

I understand I should use the function plot.plotLoops

However, can you please give me an example on the parameter loops in the function. Is it a dataframe? Can you please point me to an example using this function with its available data?

Thanks

Hi, You can find example here: #show enhancer-promoter loops cLoops2 plot -f gm/chr21-chr21.ixy -o gm_example -bs 500 -start 38752604 -end 38839334 -triu -bw ../data/GM12878_ATAC_chr21.bw,../data/GM12878_CTCF_chr21.bw -1D -loops gm_loops.txt -beds ../data/GM12878_RoadMap_hg38_Enh_chr21.bed,../data/GM12878_RoadMap_hg38_Tss_chr21.bed,gm_peaks.bed -m obs -log -gtf ../data/gencode_v30_chr21.gtf -vmax 1 https://github.com/YaqiangCao/cLoops2/raw/master/pngs/gm_example_matrix.png

loops file: https://github.com/YaqiangCao/cLoops2/blob/master/example/test_run/gm_samp_loops.txt

loops file format: https://github.com/YaqiangCao/cLoops2#_loops.txt

Best, Yaqiang