biopipen 0.32.0__py3-none-any.whl → 0.32.3__py3-none-any.whl

biopipen/scripts/scrna/SeuratClusterStats-hists.R

@@ -6,6 +6,7 @@ log_info("hists:")
 
 do_one_hists <- function(m, case, odir, h1, each = NULL) {
     ofile <- file.path(odir, paste0(slugify(h1), ifelse(is.null(each), "", paste0("-", slugify(each))), ".png"))
+    ofile_pdf <- gsub(".png$", ".pdf", ofile)
 
     p <- ggplot(m, aes(x=!!sym(case$x))) +
         geom_histogram(
@@ -42,16 +43,20 @@ do_one_hists <- function(m, case, odir, h1, each = NULL) {
     print(p)
     dev.off()
 
+    pdf(ofile_pdf, width=devpars$width / devpars$res, height=devpars$height / devpars$res)
+    print(p)
+    dev.off()
+
     # Add report
     if (!is.null(each)) {
         add_report(
-            list(src = ofile, descr = first(m[[case$each]])),
+            list(src = ofile, descr = first(m[[case$each]]), download = ofile_pdf),
             h1 = h1,
             ui = "table_of_images"
         )
     } else {
         add_report(
-            list(kind = "image", src = ofile),
+            list(kind = "image", src = ofile, download = ofile_pdf),
             h1 = h1
         )
     }

biopipen/scripts/scrna/SeuratClusterStats-ngenes.R

@@ -14,6 +14,7 @@ do_one_ngenes <- function(name) {
     case$devpars <- list_update(ngenes_defaults$devpars, case$devpars)
 
     figfile = file.path(odir, paste0(slugify(name), ".boxplot.png"))
+    figfile_pdf = file.path(odir, paste0(slugify(name), ".boxplot.pdf"))
 
     if (!is.null(case$subset)) {
         sobj <- srtobj %>% filter(!!rlang::parse_expr(case$subset))
@@ -49,6 +50,10 @@ do_one_ngenes <- function(name) {
     print(p)
     dev.off()
 
+    pdf(figfile_pdf, width=case$devpars$width / case$devpars$res, height=case$devpars$height / case$devpars$res)
+    print(p)
+    dev.off()
+
     add_report(
         list(
             kind = "descr",
@@ -62,7 +67,7 @@ do_one_ngenes <- function(name) {
                 )
             )
         ),
-        list(kind = "image", src = figfile),
+        list(kind = "image", src = figfile, download = figfile_pdf),
         h1 = name
     )
 }

biopipen/scripts/scrna/SeuratClusterStats-stats.R

@@ -23,8 +23,11 @@ do_one_stats = function(name) {
     }
 
     figfile = file.path(odir, paste0(slugify(name), ".bar.png"))
+    figfile_pdf = file.path(odir, paste0(slugify(name), ".bar.pdf"))
     piefile = file.path(odir, paste0(slugify(name), ".pie.png"))
+    piefile_pdf = file.path(odir, paste0(slugify(name), ".pie.pdf"))
     circosfile = file.path(odir, paste0(slugify(name), ".circos.png"))
+    circosfile_pdf = file.path(odir, paste0(slugify(name), ".circos.pdf"))
     samtablefile = file.path(odir, paste0(slugify(name), ".bysample.txt"))
     tablefile = file.path(odir, paste0(slugify(name), ".txt"))
 
@@ -98,6 +101,10 @@ do_one_stats = function(name) {
     print(p)
     dev.off()
 
+    pdf(figfile_pdf, width=case$devpars$width / case$devpars$res, height=case$devpars$height / case$devpars$res)
+    print(p)
+    dev.off()
+
     add_report(
         list(
             kind = "descr",
@@ -118,7 +125,7 @@ do_one_stats = function(name) {
     add_report(
         list(
             name = "Bar Plot",
-            contents = list(list(kind = "image", src = figfile))
+            contents = list(list(kind = "image", src = figfile, download = figfile_pdf))
         ),
         h1 = name,
         ui = "tabs"
@@ -162,10 +169,14 @@ do_one_stats = function(name) {
         print(p_pie)
         dev.off()
 
+        pdf(piefile_pdf, width=case$pie_devpars$width / case$pie_devpars$res, height=case$pie_devpars$height / case$pie_devpars$res)
+        print(p_pie)
+        dev.off()
+
         add_report(
             list(
                 name = "Pie Chart",
-                contents = list(list(kind = "image", src = piefile))
+                contents = list(list(kind = "image", src = piefile, download = piefile_pdf))
             ),
             h1 = name,
             ui = "tabs"

biopipen/scripts/scrna/SeuratMap2Ref.R

@@ -378,7 +378,13 @@ for (qname in names(mapquery_args$refdata)) {
         repel = TRUE,
     ) + NoLegend()
 
-    png(file.path(outdir, paste0("UMAPs-", slugify(qname), ".png")), width = 1500, height = 700, res = 100)
+    plotfile <- file.path(outdir, paste0("UMAPs-", slugify(qname), ".png"))
+    png(plotfile, width = 1500, height = 700, res = 100)
+    print(ref_p | query_p)
+    dev.off()
+
+    plotfile_pdf <- file.path(outdir, paste0("UMAPs-", slugify(qname), ".pdf"))
+    pdf(plotfile_pdf, width = 15, height = 7)
     print(ref_p | query_p)
     dev.off()
 

biopipen/scripts/scrna/SeuratPreparing-common.R

@@ -35,10 +35,10 @@ rename_files = function(e, sample, path) {
 perform_cell_qc <- function(sobj, per_sample = FALSE) {
     log_prefix <- ifelse(per_sample, "  ", "- ")
     log_info("{log_prefix}Adding metadata for QC ...")
-    sobj$percent.mt <- PercentageFeatureSet(sobj, pattern = "^MT-")
-    sobj$percent.ribo <- PercentageFeatureSet(sobj, pattern = "^RP[SL]")
-    sobj$percent.hb <- PercentageFeatureSet(sobj, pattern = "^HB[^(P)]")
-    sobj$percent.plat <- PercentageFeatureSet(sobj, pattern = "PECAM1|PF4")
+    sobj$percent.mt <- PercentageFeatureSet(sobj, pattern = "^MT-|^Mt-|^mt-")
+    sobj$percent.ribo <- PercentageFeatureSet(sobj, pattern = "^RP[SL]|^Rp[sl]")
+    sobj$percent.hb <- PercentageFeatureSet(sobj, pattern = "^HB[^P]|^Hb[^p]")
+    sobj$percent.plat <- PercentageFeatureSet(sobj, pattern = "PECAM1|PF4|Pecam1|Pf4")
 
     if (is.null(envs$cell_qc) || length(envs$cell_qc) == 0) {
         log_warn("{log_prefix}No cell QC criteria is provided. All cells will be kept.")
@@ -97,10 +97,19 @@ report_cell_qc = function(ngenes) {
         print(vln_p)
         dev.off()
 
+        vlnplot_pdf = file.path(plotsdir, paste0(slugify(feat), ".vln.pdf"))
+        pdf(
+            vlnplot_pdf,
+            width = (800 + length(samples) * 15) / 100, height = 600 / 100
+        )
+        print(vln_p)
+        dev.off()
+
         add_report(
             list(
                 src = vlnplot,
                 name = feat,
+                download = vlnplot_pdf,
                 descr = paste0("Distribution of ", feat, " for each sample.")
             ),
             h1 = "Violin Plots",
@@ -135,10 +144,16 @@ report_cell_qc = function(ngenes) {
         print(scat_p)
         dev.off()
 
+        scatfile_pdf = file.path(plotsdir, paste0(slugify(feat), "-nCount_RNA.scatter.pdf"))
+        pdf(scatfile_pdf, width = 8, height = 6)
+        print(scat_p)
+        dev.off()
+
         add_report(
             list(
                 src = scatfile,
                 name = paste0(feat, " vs nCount_RNA"),
+                download = scatfile_pdf,
                 descr = paste0("Scatter plot for ", feat, " against nCount_RNA")
             ),
             h1 = "Scatter Plots",
@@ -210,7 +225,7 @@ load_sample = function(sample) {
 
     if (isTRUE(envs$cell_qc_per_sample)) {
         log_info("- Perform cell QC for sample: {sample} ...")
-        obj = perform_cell_qc(obj, TRUE)
+        obj = perform_cell_qc(obj, per_sample = TRUE)
     }
 
     if (isTRUE(envs$use_sct)) {
@@ -287,7 +302,7 @@ run_cell_qc <- function(sobj) {
 
         if (!envs$cell_qc_per_sample) {
             log_info("Performing cell QC ...")
-            sobj = perform_cell_qc(sobj)
+            sobj = perform_cell_qc(sobj, per_sample = FALSE)
         }
 
         cached$data <- list(sobj = sobj, cell_qc_df = cell_qc_df)

biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R

@@ -158,6 +158,7 @@ plot_dd <- function(sobj, dd, detector) {
         sobj, group.by = paste0(detector, "_DropletType"), order = "doublet",
         cols = c("#333333", "#FF3333"), pt.size = 0.8, alpha = 0.5)
     ggsave(dimp, filename = file.path(plotsdir, paste0(detector, "_dimplot.png")))
+    ggsave(dimp, filename = file.path(plotsdir, paste0(detector, "_dimplot.pdf")))
 }
 
 filter_dd <- function(sobj, dd, detector) {
@@ -184,15 +185,17 @@ report_dd <- function(detector) {
 
     if (detector == "DoubletFinder") {
         add_report(
-            list(name = "pK vs BCmetric", src = file.path(plotsdir, "pK_BCmetric.png")),
-            list(name = "Dimension Reduction Plot", src = file.path(plotsdir, "DoubletFinder_dimplot.png")),
+            list(name = "pK vs BCmetric", src = file.path(plotsdir, "DoubletFinder_pK_BCmetric.png")),
+            list(name = "Dimension Reduction Plot", src = file.path(plotsdir, "DoubletFinder_dimplot.png"),
+                 download = file.path(plotsdir, "DoubletFinder_dimplot.pdf")),
             ui = "table_of_images",
             h1 = "DoubletFinder Results",
             h2 = "Plots"
         )
     } else {
         add_report(
-            list(name = "Dimension Reduction Plot",src = file.path(plotsdir, "scDblFinder_dimplot.png")),
+            list(name = "Dimension Reduction Plot", src = file.path(plotsdir, "scDblFinder_dimplot.png"),
+                 download = file.path(plotsdir, "scDblFinder_dimplot.pdf")),
             ui = "table_of_images",
             h1 = "scDblFinder Results",
             h2 = "Plots"

biopipen/scripts/scrna/TopExpressingGenes.R

@@ -161,14 +161,16 @@ do_enrich <- function(expr, odir) {
             next
         }
 
-        png(
-            file.path(odir, paste0("Enrichr-", db, ".png")),
-            res = 100, height = 1000, width = 1000
-        )
-        print(
-            plotEnrich(enriched[[db]], showTerms = 20, title = db) +
+        enrich_p <- plotEnrich(enriched[[db]], showTerms = 20, title = db) +
             theme_prism()
-        )
+        enrich_plot <- file.path(odir, paste0("Enrichr-", db, ".png"))
+        png(enrich_plot, res = 100, height = 1000, width = 1000)
+        print(enrich_p)
+        dev.off()
+
+        enrich_plot_pdf <- file.path(odir, paste0("Enrichr-", db, ".pdf"))
+        pdf(enrich_plot_pdf, height = 10, width = 10)
+        print(enrich_p)
         dev.off()
     }
 }

biopipen/scripts/tcr/CDR3AAPhyschem.R

@@ -385,6 +385,10 @@ do_one_subset = function(s) {
     print(g)
     dev.off()
 
+    pdf(file.path(odir, "estimated_coefficients.pdf"), width=10, height=10)
+    print(g)
+    dev.off()
+
     add_report(
         list(
             kind = "descr",
@@ -408,7 +412,8 @@ do_one_subset = function(s) {
             contents = list(
                 list(
                     kind = "image",
-                    src = file.path(odir, "estimated_coefficients.png")
+                    src = file.path(odir, "estimated_coefficients.png"),
+                    download = file.path(odir, "estimated_coefficients.pdf")
                 )
             )
         ),
@@ -465,6 +470,10 @@ do_one_subset = function(s) {
     print(g)
     dev.off()
 
+    pdf(file.path(odir, "distribution.pdf"), width=10, height=10)
+    print(g)
+    dev.off()
+
     add_report(
         list(
             kind = "table_image",
@@ -473,7 +482,8 @@ do_one_subset = function(s) {
                 "then scaled to have a mean of 0 and a variance of 1. ",
                 "Horizontal lines depict the mean for each population"
             ),
-            src = file.path(odir, "distribution.png")
+            src = file.path(odir, "distribution.png"),
+            download = file.path(odir, "distribution.pdf")
         ),
         h1 = ifelse(
             is.null(s),

biopipen/scripts/tcr/CloneResidency.R

@@ -500,10 +500,16 @@ handle_subject <- function(i, subjects, casename, case) {
         print(scatter_p)
         dev.off()
 
+        scatter_pdf <- gsub(".png$", ".pdf", scatter_png)
+        pdf(scatter_pdf, width = 10, height = 8)
+        print(scatter_p)
+        dev.off()
+
         add_report(
             list(
                 name = paste0(subject, " (", pair[1], " - ", pair[2], ")"),
-                src = scatter_png
+                src = scatter_png,
+                download = scatter_pdf
             ),
             h1 = h$h1,
             h2 = h$h2,
@@ -515,13 +521,19 @@ handle_subject <- function(i, subjects, casename, case) {
     # upset/venn
     venn_dir <- file.path(casedir, "venn")
     venn_png <- file.path(venn_dir, paste0("venn_", slugify(subject), ".png"))
+    venn_pdf <- gsub(".png$", ".pdf", venn_png)
+    p <- plot_venndg(counts, groups, singletons)
     png(venn_png, res = 100, height = 600, width = 800)
-    print(plot_venndg(counts, groups, singletons))
+    print(p)
+    dev.off()
+
+    pdf(venn_pdf, width = 8, height = 6)
+    print(p)
     dev.off()
 
     h <- headings(case$section, casename, "Overlapping Clones (Venn Diagram)")
     add_report(
-        list(src = venn_png, name = subject),
+        list(src = venn_png, name = subject, download = venn_pdf),
         h1 = h$h1,
         h2 = h$h2,
         h3 = h$h3,
@@ -530,13 +542,19 @@ handle_subject <- function(i, subjects, casename, case) {
 
     upset_dir <- file.path(casedir, "upset")
     upset_png <- file.path(upset_dir, paste0("upset_", slugify(subject), ".png"))
+    upset_pdf <- gsub(".png$", ".pdf", upset_png)
+    p <- plot_upset(counts, singletons, case$upset_ymax, case$upset_trans)
     png(upset_png, res = 100, height = 600, width = 800)
-    print(plot_upset(counts, singletons, case$upset_ymax, case$upset_trans))
+    print(p)
+    dev.off()
+
+    pdf(upset_pdf, width = 8, height = 6)
+    print(p)
     dev.off()
 
     h <- headings(case$section, casename, "Overlapping Clones (UpSet Plots)")
     add_report(
-        list(src = upset_png, name = subject),
+        list(src = upset_png, name = subject, download = upset_pdf),
         h1 = h$h1,
         h2 = h$h2,
         h3 = h$h3,

biopipen/scripts/tcr/Immunarch-basic.R

@@ -63,15 +63,22 @@ do_one_case_basic = function(name, case, method) {
     } else {
         p = vis(exp, .by = case$by, .meta = d$meta)
     }
+
     ofig = file.path(odir, paste0(name, ".png"))
     png(ofig, width = case$devpars$width, height = case$devpars$height, res = case$devpars$res)
     print(p + scale_fill_biopipen())
     dev.off()
 
+    ofig_pdf = file.path(odir, paste0(name, ".pdf"))
+    pdf(ofig_pdf, width = case$devpars$width / case$devpars$res, height = case$devpars$height / case$devpars$res)
+    print(p + scale_fill_biopipen())
+    dev.off()
+
     add_report(
         list(
             src = ofig,
-            name = if (name == "DEFAULT") NULL else name
+            name = if (name == "DEFAULT") NULL else name,
+            download = ofig_pdf
         ),
         h1 = "Exploratory Analysis",
         h2 = switch(method,

biopipen/scripts/tcr/Immunarch-clonality.R

@@ -78,6 +78,11 @@ do_one_case_clonality = function(name, case, method) {
     print(p)
     dev.off()
 
+    ofig_pdf = file.path(odir, paste0(name, ".pdf"))
+    pdf(ofig_pdf, width = case$devpars$width / case$devpars$res, height = case$devpars$height / case$devpars$res)
+    print(p)
+    dev.off()
+
     add_report(
         list(
             src = ofig,

biopipen/scripts/tcr/Immunarch-diversity.R

@@ -353,7 +353,14 @@ run_general = function(casename, d, case, ddir, value_col = "Value") {
             width = width * case$ncol
         }
     }
-    png(file.path(ddir, "diversity.png"), width = width, height = height, res = res)
+
+    div_plot = file.path(ddir, "diversity.png")
+    png(div_plot, width = width, height = height, res = res)
+    print(p)
+    dev.off()
+
+    div_plot_pdf = file.path(ddir, "diversity.pdf")
+    pdf(div_plot_pdf, width = width / res, height = height / res)
     print(p)
     dev.off()
 
@@ -407,7 +414,7 @@ run_general = function(casename, d, case, ddir, value_col = "Value") {
     add_report(
         list(
             name = "Diversity Plot",
-            contents = list(list(kind = "image", src = file.path(ddir, "diversity.png")))
+            contents = list(list(kind = "image", src = div_plot, download = div_plot_pdf))
         ),
         list(
             name = "Diversity Table",
@@ -559,6 +566,10 @@ run_raref_single = function(d, case, ddir, suffix = "", save_p = TRUE) {
         png(file.path(ddir, "raref.png"), width = devpars$width, height = devpars$height, res = devpars$res)
         print(p)
         dev.off()
+
+        pdf(file.path(ddir, "raref.pdf"), width = devpars$width / devpars$res, height = devpars$height / devpars$res)
+        print(p)
+        dev.off()
     } else {
         return (list(p = p, width = devpars$width))
     }
@@ -628,6 +639,14 @@ run_raref_multi = function(d, case, ddir) {
     )
     print(p)
     dev.off()
+
+    pdf(
+        file.path(ddir, paste0("raref-", slugify(case$separate_by), ".pdf")),
+        width = width / res,
+        height = height / res
+    )
+    print(p)
+    dev.off()
 }
 
 # Run the diversity estimation for one case
@@ -673,7 +692,8 @@ run_div_case = function(casename) {
             add_report(
                 list(
                     kind = "image",
-                    src = file.path(ddir, paste0("raref-", slugify(case$separate_by), ".png"))
+                    src = file.path(ddir, paste0("raref-", slugify(case$separate_by), ".png")),
+                    download = file.path(ddir, paste0("raref-", slugify(case$separate_by), ".pdf"))
                 ),
                 h1 = "Rarefraction",
                 h2 = casename
@@ -683,7 +703,8 @@ run_div_case = function(casename) {
             add_report(
                 list(
                     kind = "image",
-                    src = file.path(ddir, "raref.png")
+                    src = file.path(ddir, "raref.png"),
+                    download = file.path(ddir, "raref.pdf")
                 ),
                 h1 = "Rarefraction",
                 h2 = casename

biopipen/scripts/tcr/Immunarch-geneusage.R

@@ -126,10 +126,16 @@ do_one_case_geneusage = function(name, case, gu_dir) {
     print(p + scale_fill_biopipen())
     dev.off()
 
+    ofig_pdf = file.path(odir, paste0(name, ".pdf"))
+    pdf(ofig_pdf, width = case$devpars$width / case$devpars$res, height = case$devpars$height / case$devpars$res)
+    print(p + scale_fill_biopipen())
+    dev.off()
+
     add_report(
         list(
             kind = "table_image",
             src = ofig,
+            download = ofig_pdf,
             descr = paste0(
                  "Distribution of known gene segments following the ",
                  '<a href="http://www.imgt.org/IMGTrepertoire/LocusGenes/" target="_blank">IMGT</a> ',
@@ -165,15 +171,23 @@ do_one_case_geneusage = function(name, case, gu_dir) {
             ap = do_call(vis, avis_args)
             if (aname == "DEFAULT") {
                 aofig = file.path(odir, paste0(name, "-analysis.png"))
+                aofig_pdf = file.path(odir, paste0(name, "-analysis.pdf"))
             } else {
                 aofig = file.path(odir, paste0(name, "-", aname, "-analysis.png"))
+                aofig_pdf = file.path(odir, paste0(name, "-", aname, "-analysis.pdf"))
             }
             png(aofig, width = case$analyses$cases[[aname]]$devpars$width, height = case$analyses$cases[[aname]]$devpars$height, res = case$analyses$cases[[aname]]$devpars$res)
             print(ap)
             dev.off()
 
+            pdf(aofig_pdf,
+                width = case$analyses$cases[[aname]]$devpars$width / case$analyses$cases[[aname]]$devpars$res,
+                height = case$analyses$cases[[aname]]$devpars$height / case$analyses$cases[[aname]]$devpars$res)
+            print(ap)
+            dev.off()
+
             add_report(
-                list(src = aofig, name = aname),
+                list(src = aofig, name = aname, download = aofig_pdf),
                 h1 = "Gene Usage",
                 h2 = ifelse(name == "DEFAULT", "#", name),
                 h3 = "Gene Usage Analysis",

biopipen/scripts/tcr/Immunarch-kmer.R

@@ -105,6 +105,11 @@ do_one_case_kmer = function(name, case, kmer_dir) {
     print(p)
     dev.off()
 
+    ofig_pdf = file.path(odir, "Allsamples.pdf")
+    pdf(ofig_pdf, width = case$devpars$width / case$devpars$res, height = case$devpars$height / case$devpars$res)
+    print(p)
+    dev.off()
+
     add_report(
         list(
             kind = "descr",
@@ -116,7 +121,7 @@ do_one_case_kmer = function(name, case, kmer_dir) {
     )
 
     add_report(
-        list(kind = "image", src = ofig),
+        list(kind = "image", src = ofig, download = ofig_pdf),
         h1 = "Kmer and sequence motif analysis",
         h2 = ifelse(name == "DEFAULT", "#", name),
         h3 = "Kmer sequence occurrences"
@@ -150,9 +155,17 @@ do_one_case_kmer = function(name, case, kmer_dir) {
                 print(ap)
                 dev.off()
 
+                aofig_pdf = gsub(".png$", ".pdf", aofig)
+                pdf(aofig_pdf,
+                    width = case$profiles$cases[[aname]]$devpars$width / case$profiles$cases[[aname]]$devpars$res,
+                    height = case$profiles$cases[[aname]]$devpars$height / case$profiles$cases[[aname]]$devpars$res)
+                print(ap)
+                dev.off()
+
                 add_report(
                     list(
                         src = aofig,
+                        download = aofig_pdf,
                         name = paste0(sample, ifelse(aname == "DEFAULT", "", paste0(" - ", aname)))
                     ),
                     h1 = "Kmer and sequence motif analysis",

biopipen/scripts/tcr/Immunarch-overlap.R

@@ -138,10 +138,16 @@ do_one_case_overlap = function(name, case, ov_dir) {
     print(p)
     dev.off()
 
+    ofig_pdf = file.path(odir, paste0(name, ".pdf"))
+    pdf(ofig_pdf, width = case$devpars$width / case$devpars$res, height = case$devpars$height / case$devpars$res)
+    print(p)
+    dev.off()
+
     add_report(
         list(
             kind = "table_image",
             src = ofig,
+            download = ofig_pdf,
             descr = paste0(
                 "Repertoire overlap is the most common approach to measure repertoire similarity, ",
                 "using method <code>", case$method, "</code>, ",
@@ -179,15 +185,23 @@ do_one_case_overlap = function(name, case, ov_dir) {
             ap = do_call(vis, avis_args)
             if (aname == "DEFAULT") {
                 aofig = file.path(odir, paste0(name, "-analysis.png"))
+                aofig_pdf = file.path(odir, paste0(name, "-analysis.pdf"))
             } else {
                 aofig = file.path(odir, paste0(name, "-", aname, "-analysis.png"))
+                aofig_pdf = file.path(odir, paste0(name, "-", aname, "-analysis.pdf"))
             }
             png(aofig, width = case$analyses$cases[[aname]]$devpars$width, height = case$analyses$cases[[aname]]$devpars$height, res = case$analyses$cases[[aname]]$devpars$res)
             print(ap)
             dev.off()
 
+            pdf(aofig_pdf,
+                width = case$analyses$cases[[aname]]$devpars$width / case$analyses$cases[[aname]]$devpars$res,
+                height = case$analyses$cases[[aname]]$devpars$height / case$analyses$cases[[aname]]$devpars$res)
+            print(ap)
+            dev.off()
+
             add_report(
-                list(src = aofig, name = aname),
+                list(src = aofig, name = aname, download = aofig_pdf),
                 h1 = "Repertoire Overlaps",
                 h2 = ifelse(name == "DEFAULT", "#", name),
                 h3 = "Repertoire Overlap Analysis",

biopipen/scripts/tcr/Immunarch-spectratyping.R

@@ -69,8 +69,17 @@ do_one_case_spectratyping = function(name, case, spect_dir) {
         print(vis(spec_obj))
         dev.off()
 
+        spectfile_pdf = file.path(odir, paste0(slugify(sample), ".spect.pdf"))
+        pdf(
+            spectfile_pdf,
+            width = case$devpars$width / case$devpars$res,
+            height = case$devpars$height / case$devpars$res
+        )
+        print(vis(spec_obj))
+        dev.off()
+
         add_report(
-            list(src = spectfile, name = sample),
+            list(src = spectfile, name = sample, download = spectfile_pdf),
             h1 = "Spectratyping",
             h2 = name,
             ui = "table_of_images"

biopipen/scripts/tcr/Immunarch-tracking.R

@@ -88,6 +88,11 @@ run_tracking_case = function(casename) {
         print(vis(imm_tracking))
         dev.off()
 
+        tracking_pdf = file.path(tracking_dir, paste0(slugify(casename), ".pdf"))
+        pdf(tracking_pdf, height=10, width=6 + 1.5 * length(subjects))
+        print(vis(imm_tracking))
+        dev.off()
+
         add_report(
             list(
                 kind = "descr",
@@ -105,6 +110,7 @@ run_tracking_case = function(casename) {
         add_report(
             list(
                 src = tracking_png,
+                download = tracking_pdf,
                 name = if (casename == "DEFAULT") NULL else casename
             ),
             h1 = "Tracking of clonotypes",

biopipen/scripts/tcr/Immunarch-vjjunc.R

@@ -110,7 +110,40 @@ do_one_case_vjjunc <- function(name, case) {
         }, bg.border = NA) # here set bg.border to NA is important
         dev.off()
 
+        # figfile_pdf <- file.path(odir, paste0(slugify(by_name), ".pdf"))
+        # png(figfile_pdf, width = case$devpars$width / case$devpars$res, height = case$devpars$height / case$devpars$res)
+        # circos.clear()
+        # tryCatch({
+        #     chordDiagram(
+        #         gsd,
+        #         annotationTrack = c("grid", "axis"),
+        #         preAllocateTracks = list(track.height = 0.25)
+        #     )
+        # }, error = function(e) {
+        #     log_warn("Error encountered: {e$message}, setting gap.after ...")
+        #     circos.par(gap.after = c(rep(1, nrow(gsd) - 1), 5, rep(1, nrow(gsd) - 1), 5))
+        #     chordDiagram(
+        #         gsd,
+        #         annotationTrack = c("grid", "axis"),
+        #         preAllocateTracks = list(track.height = 0.25)
+        #     )
+
+        # })
+        # circos.track(track.index = 1, panel.fun = function(x, y) {
+        #     circos.text(
+        #         CELL_META$xcenter,
+        #         CELL_META$ylim[1],
+        #         CELL_META$sector.index,
+        #         cex = .8,
+        #         facing = "clockwise",
+        #         niceFacing = TRUE,
+        #         adj = c(-0.2, 0.5)
+        #     )
+        # }, bg.border = NA) # here set bg.border to NA is important
+        # dev.off()
+
         add_report(
+            # list(src = figfile, name = by_name, download = figfile_pdf),
             list(src = figfile, name = by_name),
             h1 = "V-J Junction Circos Plots",
             h2 = ifelse(name == "DEFAULT", "#" , name),