Question: deeptools plotHeatmap gives blurry pixelated image
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gravatar for Himanshu C
5 weeks ago by
Himanshu C0
Norris Cotton Cancer Center | DHMC
Himanshu C0 wrote:

Hi, I'm using deeptools to visualize bigWig files, my commands:

computeMatrix scale-regions -S bigWigs/batch1and3/*.bw -R /ATAC_12-4-20/diffBind_results/*.bed  --skipZeros -p 10 --missingDataAsZero -a 500 -b 500 -o batch1and3_As_Con_sites_new_w_blklist.gz -bs 1 --blackListFileName remapped_Blacklist_ZF_Grcz10_toGrcz11.txt

plotHeatmap -m batch1and3_As_Con_sites_new_w_blklist.gz -out batch1and3_As_Con_sites_heatmapProfile_updated_w_blk_lists.pdf --startLabel "" --endLabel "" --colorMap Blues --dpi 600  --samplesLabel "As_rep1" "As_rep2" "Con_rep1" "Con_rep2" --xAxisLabel "" --legendLocation upper-center --zMin 0 --zMax 30 --legendLocation "none" --regionsLabel "As-Upregulated" "As-Downregulated" --interpolationMethod "nearest"

batch1and3-As-Con-sites-heatmap-Profile-updated-w-blk-lists

I'm getting a blurred heatmap. Is it because of relatively fewer regions? How can it be fixed? Thanks

Edit: Found the solution: "--heatmapHeight" did the trick!

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Himanshu C0

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ADD REPLYlink written 5 weeks ago by GenoMax96k
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