biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/scripts/tcr/Immunarch-geneusage.R

@@ -1,9 +1,12 @@
 # loaded variables
 # immfile, outdir, mutaters, immdata, n_samples
 
-gene_usages = {{ envs.gene_usages | r: todot="-" }}
+log_info("")
+log_info("# Gene usage analysis")
+log_info("-----------------------------------")
 
 # Fill up cases
+log_info("Filling up cases ...")
 cases = gene_usages$cases
 if (is.null(cases) || length(cases) == 0) {
     cases$DEFAULT = list(
@@ -92,7 +95,8 @@ for (name in names(cases)) {
 }
 
 do_one_case_geneusage = function(name, case, gu_dir) {
-    print(paste0("  Case: ", name))
+    # print(paste0("  Case: ", name))
+    log_info("Processing case: {name} ...")
     odir = file.path(gu_dir, name)
     dir.create(odir, showWarnings = FALSE)
 
@@ -119,15 +123,36 @@ do_one_case_geneusage = function(name, case, gu_dir) {
 
     ofig = file.path(odir, paste0(name, ".png"))
     png(ofig, width = case$devpars$width, height = case$devpars$height, res = case$devpars$res)
-    print(p)
+    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> ',
+                 "nomenclature."
+            )
+        ),
+        h1 = "Gene Usage",
+        h2 = ifelse(name == "DEFAULT", "#", name)
+    )
+
     if (!is.null(case$analyses$cases) && length(case$analyses$cases) > 0) {
         for (aname in names(case$analyses$cases)) {
             if (case$analyses$cases[[aname]]$method == "none") {
                 next
             }
-            print(paste0("    Analysis: ", aname))
+            # print(paste0("    Analysis: ", aname))
+            log_info("- Processing analysis: {aname} ...")
             tryCatch({
                 imm_gua = geneUsageAnalysis(imm_gu, .method = case$analyses$cases[[aname]]$method)
             }, error = function(e) {
@@ -146,12 +171,28 @@ 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, download = aofig_pdf),
+                h1 = "Gene Usage",
+                h2 = ifelse(name == "DEFAULT", "#", name),
+                h3 = "Gene Usage Analysis",
+                ui = "table_of_images"
+            )
         }
     }
 }
@@ -159,7 +200,6 @@ do_one_case_geneusage = function(name, case, gu_dir) {
 gu_dir = file.path(outdir, "gene_usage")
 dir.create(gu_dir, showWarnings = FALSE)
 
-print("- Gene usage")
 for (name in names(cases)) {
     do_one_case_geneusage(name, cases[[name]], gu_dir)
 }

biopipen/scripts/tcr/Immunarch-kmer.R

@@ -1,9 +1,12 @@
 # loaded variables
 # immfile, outdir, mutaters, immdata, n_samples
 
-kmers = {{ envs.kmers | r: todot="-" }}
+log_info("")
+log_info("# K-mer analysis")
+log_info("-----------------------------------")
 
 # Fill up cases
+log_info("Filling up cases ...")
 cases = kmers$cases
 if (is.null(cases) || length(cases) == 0) {
     cases$DEFAULT = list(
@@ -80,8 +83,9 @@ for (name in names(cases)) {
 }
 
 do_one_case_kmer = function(name, case, kmer_dir) {
-    print(paste0("  Case: ", name))
-    odir = file.path(kmer_dir, name)
+    # print(paste0("  Case: ", name))
+    log_info("Processing case: {name} ...")
+    odir = file.path(kmer_dir, slugify(name))
     dir.create(odir, showWarnings = FALSE)
 
     if (!is.null(case$subset)) {
@@ -101,34 +105,90 @@ 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",
+            content = "K-mer sequence occurrences and motif analysis of CDR3 amino acid sequences"
+        ),
+        h1 = "Kmer and sequence motif analysis",
+        h2 = ifelse(name == "DEFAULT", "#", name),
+        h3 = "Kmer sequence occurrences"
+    )
+
+    add_report(
+        list(kind = "image", src = ofig, download = ofig_pdf),
+        h1 = "Kmer and sequence motif analysis",
+        h2 = ifelse(name == "DEFAULT", "#", name),
+        h3 = "Kmer sequence occurrences"
+    )
+
+    add_report(
+        h1 = "Kmer and sequence motif analysis",
+        h2 = ifelse(name == "DEFAULT", "#", name),
+        h3 = "Motif analysis"
+    )
+
     for (sample in names(d$data)) {
-        print(paste0("    Sample: ", sample))
+        # print(paste0("    Sample: ", sample))
+        log_info("- Sample: {sample} ...")
         imm_kmer = getKmers(d$data[[sample]], case$k)
 
         if (!is.null(case$profiles$cases) && length(case$profiles$cases) > 0) {
             for (aname in names(case$profiles$cases)) {
-                print(paste0("    Profiling: ", aname))
+                # print(paste0("    Profiling: ", aname))
+                log_info("  Profiling: {aname} ...")
                 imm_kmera = kmer_profile(imm_kmer, case$profiles$cases[[aname]]$method)
                 avis_args = case$profiles$cases[[aname]]$vis_args
                 avis_args$.data = imm_kmera
                 ap = do_call(vis, avis_args)
                 if (aname == "DEFAULT") {
-                    aofig = file.path(odir, paste0(sample, "-profile.png"))
+                    aofig = file.path(odir, paste0(slugify(sample), "-profile.png"))
                 } else {
-                    aofig = file.path(odir, paste0(sample, "-", aname, "-profile.png"))
+                    aofig = file.path(odir, paste0(slugify(sample), "-", slugify(aname), "-profile.png"))
                 }
                 png(aofig, width = case$profiles$cases[[aname]]$devpars$width, height = case$profiles$cases[[aname]]$devpars$height, res = case$profiles$cases[[aname]]$devpars$res)
                 print(ap)
                 dev.off()
+
+                aofig_pdf = gsub(".png$", ".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",
+                    h2 = ifelse(name == "DEFAULT", "#", name),
+                    h3 = "Motif analysis",
+                    ui = "table_of_images"
+                )
             }
         }
     }
 }
 
+add_report(
+    list(
+        kind = "descr",
+        content = "Counting k-mer occurrences"
+    ),
+    h1 = "Kmer and sequence motif analysis"
+)
+
 kmer_dir = file.path(outdir, "kmer")
 dir.create(kmer_dir, showWarnings = FALSE)
 
-print("- K-mer analysis")
 for (name in names(cases)) {
     do_one_case_kmer(name, cases[[name]], kmer_dir)
 }

biopipen/scripts/tcr/Immunarch-overlap.R

@@ -1,7 +1,9 @@
 # loaded variables
 # immfile, outdir, mutaters, immdata, n_samples
 
-overlaps = {{ envs.overlaps | r: todot="-" }}
+log_info("")
+log_info("# Overlap analysis")
+log_info("-----------------------------------")
 
 # Fill up cases
 cases = overlaps$cases
@@ -75,8 +77,48 @@ for (name in names(cases)) {
     cases[[name]]$analyses = analyses
 }
 
+get_method_descr <- function(method) {
+    descr <- switch(method,
+        public = paste0(
+            "number of public (shared) clonotypes, ",
+            "a classic measure of overlap similarity"
+        ),
+        overlap = paste0(
+            "overlap coefficient, a normalised measure of overlap similarity. ",
+            "It is defined as the size of the intersection divided by the smaller of ",
+            "the size of the two sets."
+        ),
+        jaccard = paste0(
+            "Jaccard index, measures the similarity between finite sample sets, ",
+            "and is defined as the size of the intersection divided by the size of ",
+            "the union of the sample sets."
+        ),
+        tversky = paste0(
+            "Tversky index, an asymmetric similarity measure on sets that compares ",
+            "a variant to a prototype. ",
+            "If using default arguments, it’s similar to Dice’s coefficient."
+        ),
+        cosine = "cosine similarity, a measure of similarity between two non-zero vectors",
+        morisita = paste0(
+            "Morisita's overlap index, a statistical measure of dispersion of ",
+            "individuals in a population. ",
+            "It is used to compare overlap among samples."
+        )
+    )
+
+    if (!is.null(descr)) {
+        return(descr)
+    }
+
+    return(paste0(
+        "incremental overlap, ",
+        "overlaps of the N most abundant clonotypes with incrementally growing N"
+    ))
+}
+
 do_one_case_overlap = function(name, case, ov_dir) {
-    print(paste0("  Case: ", name))
+    # print(paste0("  Case: ", name))
+    log_info("Processing case: {name} ...")
     odir = file.path(ov_dir, name)
     dir.create(odir, showWarnings = FALSE)
 
@@ -96,11 +138,32 @@ 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$method, "</code>, ",
+                get_method_descr(case$method)
+            )
+        ),
+        h1 = "Repertoire Overlaps",
+        h2 = ifelse(name == "DEFAULT", "#", name)
+    )
+
     if (!is.null(case$analyses$cases) && length(case$analyses$cases) > 0) {
         for (aname in names(case$analyses$cases)) {
             if (case$analyses$cases[[aname]]$method == "none") next
 
-            print(paste0("    Analysis: ", aname))
+            # print(paste0("    Analysis: ", aname))
+            log_info("- Processing analysis: {aname} ...")
             k = min(n_samples - 1, 2)
             tryCatch({
                 imm_ova = repOverlapAnalysis(
@@ -122,12 +185,29 @@ 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, download = aofig_pdf),
+                h1 = "Repertoire Overlaps",
+                h2 = ifelse(name == "DEFAULT", "#", name),
+                h3 = "Repertoire Overlap Analysis",
+                ui = "table_of_images"
+            )
+
         }
     }
 }
@@ -135,7 +215,7 @@ do_one_case_overlap = function(name, case, ov_dir) {
 ov_dir = file.path(outdir, "overlap")
 dir.create(ov_dir, showWarnings = FALSE)
 
-print("- Overlap")
+# print("- Overlap")
 for (name in names(cases)) {
     do_one_case_overlap(name, cases[[name]], ov_dir)
 }

biopipen/scripts/tcr/Immunarch-spectratyping.R

@@ -1,9 +1,12 @@
 # loaded variables
 # immfile, outdir, mutaters, immdata, n_samples
 
-spects = {{ envs.spects | r }}
+log_info("")
+log_info("# Spectratyping analysis")
+log_info("-----------------------------------")
 
 # Fill up cases
+log_info("Filling up cases ...")
 if (is.null(spects$cases) || length(spects$cases) == 0) {
     spects$cases$DEFAULT = list(
         quant = spects$quant,
@@ -37,8 +40,9 @@ if (is.null(spects$cases) || length(spects$cases) == 0) {
 }
 
 do_one_case_spectratyping = function(name, case, spect_dir) {
-    print(paste0("  Case: ", name))
-    odir = file.path(spect_dir, name)
+    # print(paste0("  Case: ", name))
+    log_info("- Processing case: {name} ...")
+    odir = file.path(spect_dir, slugify(name))
     dir.create(odir, showWarnings = FALSE)
 
     if (!is.null(case$subset)) {
@@ -48,24 +52,49 @@ do_one_case_spectratyping = function(name, case, spect_dir) {
     }
 
     for (sample in names(d$data)) {
-        print(paste0("    Sample: ", sample))
+        # print(paste0("    Sample: ", sample))
+        log_info("  Sample: {sample} ...")
         spec_obj = spectratype(
             d$data[[sample]],
             .quant = case$quant,
             .col = case$col
         )
+        spectfile = file.path(odir, paste0(slugify(sample), ".spect.png"))
         png(
-            file.path(odir, paste0(sample, ".png")),
+            spectfile,
             res = case$devpars$res,
             width = case$devpars$width,
             height = case$devpars$height
         )
         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, download = spectfile_pdf),
+            h1 = "Spectratyping",
+            h2 = name,
+            ui = "table_of_images"
+        )
     }
 }
 
-print("- Spectratyping")
+add_report(
+    list(
+        kind = "descr",
+        content = "Spectratype is a useful way to represent distributions of genes per sequence length."
+    ),
+    h1 = "Spectratyping"
+)
+
 spect_dir = file.path(outdir, "spectratyping")
 dir.create(spect_dir, showWarnings = FALSE)
 

biopipen/scripts/tcr/Immunarch-tracking.R

@@ -1,7 +1,8 @@
-print("- Clonotype tracking")
-
-trackings = {{ envs.trackings | r }}
+log_info("")
+log_info("# Clonotype tracking")
+log_info("-----------------------------------")
 
+log_info("Filling up cases ...")
 if (is.null(trackings$subjects)) {
     trackings$subjects = c()
 }
@@ -41,9 +42,11 @@ run_tracking_case = function(casename) {
     }
 
     if (is.null(case$targets)) {
-        print(paste0("  ", casename, ", skip, no targets"))
+        # print(paste0("  ", casename, ", skip, no targets"))
+        log_info("- Case: {casename}, skip, no targets")
     } else {
-        print(paste0("  ", casename))
+        # print(paste0("  ", casename))
+        log_info("- Case: {casename}")
         allsubjects = d$meta %>% pull(case$subject_col) %>% unlist() %>% unique() %>% na.omit()
         if (is.null(case$subjects) || length(case$subjects) == 0) {
             subjects = allsubjects
@@ -80,10 +83,39 @@ run_tracking_case = function(casename) {
             imm_tracking = trackClonotypes(newdata, targets, .col = "aa")
         }
 
-        tracking_png = file.path(tracking_dir, paste0(casename, ".png"))
+        tracking_png = file.path(tracking_dir, paste0(slugify(casename), ".png"))
         png(tracking_png, res=100, height=1000, width=600 + 150 * length(subjects))
         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",
+                content = paste0(
+                    "Clonotype tracking is a popular approach to monitor changes in the frequency of ",
+                    "clonotypes of interest in vaccination and cancer immunology. ",
+                    "For example, a researcher can track a clonotype across different time points ",
+                    "in pre- and post-vaccination repertoires, or analyse the growth of ",
+                    "malignant clonotypes in a tumor sample."
+                )
+            ),
+            h1 = "Tracking of clonotypes"
+        )
+
+        add_report(
+            list(
+                src = tracking_png,
+                download = tracking_pdf,
+                name = if (casename == "DEFAULT") NULL else casename
+            ),
+            h1 = "Tracking of clonotypes",
+            ui = "table_of_images"
+        )
     }
 }
 

biopipen/scripts/tcr/Immunarch-vjjunc.R

@@ -0,0 +1,165 @@
+log_info("")
+log_info("# VJ Junction Circos Plots")
+log_info("-----------------------------------")
+
+# Already required by immunarch
+library(circlize)
+
+log_info("Filling up cases ...")
+cases <- vj_juncs$cases
+if (is.null(cases) || length(cases) == 0) {
+    cases$DEFAULT <- list(
+        by = vj_juncs$by,
+        by_clones = vj_juncs$by_clones,
+        subset = vj_juncs$subset,
+        devpars = vj_juncs$devpars
+    )
+} else {
+    for (name in names(cases)) {
+        if (is.null(cases[[name]]$by)) {
+            cases[[name]]$by <- vj_juncs$by
+        }
+        if (is.null(cases[[name]]$by_clones)) {
+            cases[[name]]$by_clones <- vj_juncs$by_clones
+        }
+        if (is.null(cases[[name]]$subset)) {
+            cases[[name]]$subset <- vj_juncs$subset
+        }
+        if (is.null(cases[[name]]$devpars)) {
+            cases[[name]]$devpars <- vj_juncs$devpars
+        }
+        if (is.null(cases[[name]]$devpars$width)) {
+            cases[[name]]$devpars$width <- vj_juncs$devpars$width
+        }
+        if (is.null(cases[[name]]$devpars$height)) {
+            cases[[name]]$devpars$height <- vj_juncs$devpars$height
+        }
+        if (is.null(cases[[name]]$devpars$res)) {
+            cases[[name]]$devpars$res <- vj_juncs$devpars$res
+        }
+    }
+}
+
+vjjunc_dir = file.path(outdir, "vj_junc")
+dir.create(vjjunc_dir, showWarnings = FALSE)
+
+do_one_case_vjjunc <- function(name, case) {
+    log_info("Processing case: {name} ...")
+    odir = file.path(vjjunc_dir, slugify(name))
+    dir.create(odir, showWarnings = FALSE)
+
+    if (!is.null(case$subset)) {
+        d = filter_expanded_immdata(exdata, case$subset)
+    } else {
+        d = exdata
+    }
+
+    if (is.null(case$by) || length(case$by) == 0) {
+        case$by <- "Sample"
+    }
+
+    by = trimws(strsplit(case$by, ",")[[1]])
+
+    lapply(group_split(d, !!!syms(by)), function(gsd) {
+        by_name <- gsd[1, by, drop = FALSE] %>% unlist() %>% paste0(collapse = "-")
+        log_info("- Processing {by_name} ...")
+
+        if (isTRUE(case$by_clones)) {
+            gsd <- gsd %>% distinct(CDR3.aa, .keep_all = TRUE)
+        }
+        gsd <- gsd %>%
+            group_by(V.name, J.name) %>%
+            summarise(Size = n(), .groups = "drop") %>%
+            filter(!is.na(V.name) & !is.na(J.name) & V.name != "None" & J.name != "None") %>%
+            # if it's multiple chains, then split the chains
+            separate_rows(V.name, J.name, sep = ";") %>%
+            filter(!is.na(V.name) & !is.na(J.name) & V.name != "None" & J.name != "None") %>%
+            group_by(V.name, J.name) %>%
+            summarise(Size = sum(Size), .groups = "drop") %>%
+            arrange(desc(Size), V.name, J.name)
+
+        figfile <- file.path(odir, paste0(slugify(by_name), ".png"))
+        png(figfile, width = case$devpars$width, height = case$devpars$height, res = case$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$sector.index,
+                cex = .8,
+                facing = "clockwise",
+                niceFacing = TRUE,
+                adj = c(-0.2, 0.5)
+            )
+        }, bg.border = NA) # here set bg.border to NA is important
+        dev.off()
+
+        # figfile_pdf <- file.path(odir, paste0(slugify(by_name), ".pdf"))
+        # png(figfile_pdf, width = case$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),
+            ui = "table_of_images"
+        )
+
+        NULL
+    })
+}
+
+add_report(
+    list(
+        kind = "descr",
+        content = "V-J usage plot displaying the frequency of various V-J junctions."
+    ),
+    h1 = "V-J Junction Circos Plots"
+)
+
+sapply(names(cases), function(name) do_one_case_vjjunc(name, cases[[name]]))