To calculate and crate the Open Chromatin plot we spend 20sec.
The line of code that does it is:
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# Tissue specificity plot if open signal matrix is provided |
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if (!exists("bedmeta") ){ |
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if (openSignalMatrix == "None") { |
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message("open signal matrix not provided. Skipping tissue specificity plot ... ") |
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} else { |
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tryCatch( |
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expr = { |
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plotBoth("open_chromatin", plotSummarySignal(calcSummarySignal(query, data.table::fread(openSignalMatrix))), digest, outfolder) |
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plots = rbind(plots, getPlotReportDF("open_chromatin", "Cell specific enrichment for open chromatin", digest, outfolder)) |
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message("Successfully calculated and plot cell specific enrichment for open chromatin.") |
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}, |
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error = function(e){ |
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message('Caught an error in creating: Cell specific enrichment for open chromatin plot!') |
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print(e) |
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} |
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) |
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} |
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} |
Is there a way to speed this process up?
