biopipen 0.32.0__py3-none-any.whl → 0.32.3__py3-none-any.whl
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- biopipen/__init__.py +1 -1
- biopipen/core/filters.py +45 -6
- biopipen/reports/scrna/TopExpressingGenes.svelte +1 -1
- biopipen/reports/utils/misc.liq +6 -4
- biopipen/scripts/delim/SampleInfo.R +10 -1
- biopipen/scripts/scrna/CellsDistribution.R +31 -6
- biopipen/scripts/scrna/MarkersFinder.R +67 -16
- biopipen/scripts/scrna/MetaMarkers.R +16 -7
- biopipen/scripts/scrna/RadarPlots.R +22 -2
- biopipen/scripts/scrna/ScFGSEA.R +1 -1
- biopipen/scripts/scrna/SeuratClusterStats-clustree.R +7 -1
- biopipen/scripts/scrna/SeuratClusterStats-dimplots.R +9 -2
- biopipen/scripts/scrna/SeuratClusterStats-features.R +22 -4
- biopipen/scripts/scrna/SeuratClusterStats-hists.R +7 -2
- biopipen/scripts/scrna/SeuratClusterStats-ngenes.R +6 -1
- biopipen/scripts/scrna/SeuratClusterStats-stats.R +13 -2
- biopipen/scripts/scrna/SeuratMap2Ref.R +7 -1
- biopipen/scripts/scrna/SeuratPreparing-common.R +21 -6
- biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R +6 -3
- biopipen/scripts/scrna/TopExpressingGenes.R +9 -7
- biopipen/scripts/tcr/CDR3AAPhyschem.R +12 -2
- biopipen/scripts/tcr/CloneResidency.R +23 -5
- biopipen/scripts/tcr/Immunarch-basic.R +8 -1
- biopipen/scripts/tcr/Immunarch-clonality.R +5 -0
- biopipen/scripts/tcr/Immunarch-diversity.R +25 -4
- biopipen/scripts/tcr/Immunarch-geneusage.R +15 -1
- biopipen/scripts/tcr/Immunarch-kmer.R +14 -1
- biopipen/scripts/tcr/Immunarch-overlap.R +15 -1
- biopipen/scripts/tcr/Immunarch-spectratyping.R +10 -1
- biopipen/scripts/tcr/Immunarch-tracking.R +6 -0
- biopipen/scripts/tcr/Immunarch-vjjunc.R +33 -0
- biopipen/scripts/tcr/TCRClusterStats.R +24 -7
- biopipen/scripts/tcr/TESSA.R +6 -1
- biopipen/utils/gsea.R +21 -7
- biopipen/utils/plot.R +53 -17
- {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/METADATA +3 -2
- {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/RECORD +39 -39
- {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/WHEEL +1 -1
- {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/entry_points.txt +0 -0
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@@ -69,6 +69,7 @@ cluster_size_distribution = function(name) {
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outfile = file.path(odir, "cluster_size_distribution.txt")
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outplot = file.path(odir, "cluster_size_distribution.png")
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outplot_pdf = file.path(odir, "cluster_size_distribution.pdf")
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write.table(clsizes, outfile, quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE)
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plotGG(
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@@ -82,14 +83,15 @@ cluster_size_distribution = function(name) {
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"scale_fill_biopipen()"
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),
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devpars = case$devpars,
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outfile = outplot
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outfile = c(outplot, outplot_pdf)
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)
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add_report(
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list(
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src = outplot,
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name = ifelse(name == "DEFAULT", FALSE, name),
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descr = paste0("Cluster size distribution for each ", case$by)
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descr = paste0("Cluster size distribution for each ", case$by),
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download = outplot_pdf
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),
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ui = "table_of_images",
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h1 = "Cluster Size Distribution"
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@@ -162,6 +164,8 @@ shared_clusters = function(name) {
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row_samples = samples
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}
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hmplot = file.path(odir, "shared_clusters.png")
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hmplot_pdf = file.path(odir, "shared_clusters.pdf")
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# Plot heatmap
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plotHeatmap(
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plotdata,
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}
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),
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devpars = case$devpars,
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outfile =
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outfile = c(hmplot, hmplot_pdf)
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)
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add_report(
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list(
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src =
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src = hmplot,
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download = hmplot_pdf,
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name = ifelse(name == "DEFAULT", FALSE, name),
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descr = paste0("Shared TCR clusters across samples")
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),
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@@ -219,16 +224,18 @@ shared_clusters_by_grouping = function(name) {
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}
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outfile = file.path(odir, "shared_clusters.png")
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outfile_pdf = file.path(odir, "shared_clusters.pdf")
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plotVenn(
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data,
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ggs = 'ggtitle("Shared TCR Clusters")',
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devpars = case$devpars,
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outfile = outfile
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outfile = c(outfile, outfile_pdf)
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)
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add_report(
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list(
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src = outfile,
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download = outfile_pdf,
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name = ifelse(name == "DEFAULT", FALSE, name),
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descr = paste0("Shared TCR clusters across ", grouping)
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),
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@@ -275,6 +282,7 @@ sample_diversity = function(name) {
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}
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outfile = file.path(odir, "diversity.txt")
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outplot = file.path(odir, "diversity.png")
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outplot_pdf = file.path(odir, "diversity.pdf")
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div = repDiversity(data, .method = case$method)
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write.table(
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if (ncol(div) == 1) {
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args = list(mapping = mapping),
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ggs = ggs,
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devpars = case$devpars,
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outfile = outplot
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outfile = c(outplot, outplot_pdf)
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)
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} else {
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if (is.null(case$by) || length(case$by) == 0) {
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)
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print(p)
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dev.off()
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pdf(
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outplot_pdf,
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width=case$devpars$width / case$devpars$res,
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height=case$devpars$height / case$devpars$res
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)
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print(p)
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dev.off()
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}
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add_report(
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),
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list(
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kind = "image",
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src = outplot
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src = outplot,
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download = outplot_pdf
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)
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)
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),
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biopipen/scripts/tcr/TESSA.R
CHANGED
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print(p)
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dev.off()
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pdf(file.path(result_dir, "Cluster_size_dist.pdf"), width=8, height=8)
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print(p)
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dev.off()
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add_report(
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list(
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src = file.path(result_dir, "Cluster_size_dist.png"),
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descr = "Histogram of cluster size distribution"
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descr = "Histogram of cluster size distribution",
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download = file.path(result_dir, "Cluster_size_dist.pdf")
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),
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list(
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src = file.path(result_dir, "clone_size.png"),
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biopipen/utils/gsea.R
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}
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topPathways = unlist(topPathways)
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png(tablefig, res=100, width=1000, height=200 + 40 * length(topPathways))
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print(plotGseaTable(
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p <- plotGseaTable(
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envs$pathways[topPathways],
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ranks,
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gsea_res,
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gseaParam = if (!is.null(envs$gseaParam)) envs$gseaParam else 1
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)
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)
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tablefig = file.path(outdir, "gsea_table.png")
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png(tablefig, res=100, width=1000, height=200 + 40 * length(topPathways))
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print(p)
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dev.off()
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tablefig_pdf = file.path(outdir, "gsea_table.pdf")
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pdf(tablefig_pdf, width=10, height=2 + 0.4 * length(topPathways))
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print(p)
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dev.off()
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for (pathway in topPathways) {
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enrfig = file.path(outdir, paste0("fgsea_", slugify(pathway), ".png"))
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print(plotEnrichment(
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p <- plotEnrichment(
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envs$pathways[[pathway]],
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ranks,
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gseaParam = if (!is.null(envs$gseaParam)) envs$gseaParam else 1
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) + labs(title = pathway)
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) + labs(title = pathway)
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png(enrfig, res=100, width=1000, height=800)
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print(p)
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dev.off()
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enrfig_pdf = gsub(".png$", ".pdf", enrfig)
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pdf(enrfig_pdf, width=10, height=8)
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print(p)
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dev.off()
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}
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}
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biopipen/utils/plot.R
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for (outf in outfile) {
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pdf(outf, width = devpars$width / devpars$res, height=devpars$height / devpars$res)
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print(p)
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dev.off()
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} else {
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do.call(fmt, devpars)
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print(p)
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dev.off()
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}
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}
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} else {
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pdf(outf, width = devpars$width / devpars$res, height=devpars$height / devpars$res)
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print(p)
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dev.off()
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} else {
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do.call(fmt, devpars)
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print(p)
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}
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} else {
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return(hm)
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} else if (outfile
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} else if (identical(outfile, "draw")) {
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pdf(outf, width = devpars$width / devpars$res, height=devpars$height / devpars$res)
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do.call(ComplexHeatmap::draw, c(list(hm), draw))
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} else {
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do.call(fmt, devpars)
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do.call(ComplexHeatmap::draw, c(list(hm), draw))
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dev.off()
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}
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}
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}
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Metadata-Version: 2.
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Metadata-Version: 2.3
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Name: biopipen
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Version: 0.32.
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Version: 0.32.3
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Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
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License: MIT
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Author: pwwang
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@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Provides-Extra: runinfo
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Requires-Dist: datar[pandas] (>=0.15.6,<0.16.0)
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