biopipen 0.27.8__py3-none-any.whl → 0.27.9__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.27.8"
+__version__ = "0.27.9"

biopipen/ns/tcr.py

@@ -1310,6 +1310,10 @@ class TCRClusterStats(Proc):
                 numbers on the heatmap.
             - heatmap_meta (list): The columns of metadata to show on the
                 heatmap.
+            - cluster_rows (flag): Whether to cluster the rows on the heatmap.
+            - sample_order: The order of the samples on the heatmap.
+                Either a string separated by `,` or a list of sample names.
+                This only works for columns if `cluster_rows` is `True`.
             - grouping: The groups to investigate the shared clusters.
                 If specified, venn diagrams will be drawn instead of heatmaps.
                 In such case, `numbers_on_heatmap` and `heatmap_meta` will be
@@ -1373,6 +1377,9 @@ class TCRClusterStats(Proc):
         "shared_clusters": {
             "numbers_on_heatmap": True,
             "heatmap_meta": [],
+            "cluster_rows": True,
+            "sample_order": None,
+            "cluster_rows": True,
             "grouping": None,
             "devpars": {"width": 1000, "height": 1000, "res": 100},
             "cases": {},

biopipen/scripts/tcr/TCRClusterStats.R

@@ -137,6 +137,26 @@ shared_clusters = function(name) {
         anno = do_call(ComplexHeatmap::HeatmapAnnotation, anno)
     }
 
+    if (!is.null(case$sample_order) && length(case$sample_order) > 0) {
+        if (length(case$sample_order) == 1) {
+            case$sample_order = trimws(strsplit(case$sample_order, ",")[[1]])
+        }
+        nonexisting = setdiff(case$sample_order, samples)
+        if (length(nonexisting) > 0) {
+            stop(paste("  The following samples do not exist in `sample_order`:", paste(nonexisting, collapse=", ")))
+        }
+        plotdata = plotdata[, case$sample_order, drop=FALSE]
+    }
+
+    cluster_rows = case$cluster_rows && nrow(plotdata) > 2
+    col_samples = colnames(plotdata)
+    if (!cluster_rows) {
+        plotdata = plotdata[col_samples, ]
+        row_samples = col_samples
+    } else {
+        row_samples = samples
+    }
+
     # Plot heatmap
     plotHeatmap(
         plotdata,
@@ -144,12 +164,12 @@ shared_clusters = function(name) {
             name = "Shared TCR Clusters",
             col = c("#ffe1e1", "red3"),
             cluster_columns = FALSE,
-            cluster_rows = nrow(plotdata) > 2,
+            cluster_rows = cluster_rows,
             top_annotation = anno,
             cell_fun = if (
                 is.null(case$numbers_on_heatmap) || !case$numbers_on_heatmap
             ) NULL else function(j, i, x, y, width, height, fill) {
-                grid.text(plotdata[samples[i], samples[j]], x, y, gp = gpar(fontsize = 10))
+                grid.text(row_samples[i], col_samples[j], x, y, gp = gpar(fontsize = 10))
             }
         ),
         devpars = case$devpars,

{biopipen-0.27.8.dist-info → biopipen-0.27.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.27.8
+Version: 0.27.9
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.27.8.dist-info → biopipen-0.27.9.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=tTYofCNMPRiC5Qs7KVRV32NVPrdQ2HjfgoMDf4fChsQ,23
+biopipen/__init__.py,sha256=sJWdNHkiTx9zQyc6_YJknVzen19cpBrSswdfVQaZ7S8,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=20RCI30Peee1EQdfb_UbV3Hf74XUPndJnYZlUThytsw,1781
@@ -26,7 +26,7 @@ biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwoo
 biopipen/ns/snp.py,sha256=EQ2FS0trQ7YThPmBVTpS66lc2OSfgQ6lCh6WnyP-C2g,5499
 biopipen/ns/stats.py,sha256=yJ6C1CXF84T7DDs9mgufqUOr89Rl6kybE5ji8Vnx6cw,13693
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
-biopipen/ns/tcr.py,sha256=7F_FulZ3UGouuvgH_ylZwJybr_310f9BTz_kouO1SjY,87905
+biopipen/ns/tcr.py,sha256=0PCF8iPZ629z6P3RHoAWEpMWmuDslomTGcMopjqvXmE,88304
 biopipen/ns/vcf.py,sha256=cdkKroii0_nl_bSP2cnO09qESUAhHqu6btOiTSKS79Y,15314
 biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
@@ -193,7 +193,7 @@ biopipen/scripts/tcr/ImmunarchFilter.R,sha256=o25O36FwH_0w6F8DFQ0SfpcwDzlzaGefXq
 biopipen/scripts/tcr/ImmunarchLoading.R,sha256=l_l-gojiCKI_MWgIUe2zG5boVtNipBv4rACRJEcrnFE,5734
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=jQ1OU3b8vswD8tZhLt3fkcqJKrl2bhQX0giHM2rXz3Y,2643
-biopipen/scripts/tcr/TCRClusterStats.R,sha256=D7q1svXQxl1uOya8bePvR9e6NJXjCjXbPsXnEPTWdlE,12004
+biopipen/scripts/tcr/TCRClusterStats.R,sha256=aaY9w1GZWQLVQR7wl8POGCzzW7q0ge6cWxrzmqoWNA8,12743
 biopipen/scripts/tcr/TCRClustering.R,sha256=eflUsYfq4aEaX9BVL0MiB7lNlot_L-8VaReK516go84,9236
 biopipen/scripts/tcr/TCRDock.py,sha256=jjzxMWp-hs0LDtA1mVbiWDvUieSO7X-F9yeKGy1LSTM,3026
 biopipen/scripts/tcr/TESSA.R,sha256=bfOixWLZy8yi0MzXncP67KjtCukwXEzsK5fCdMzB5VM,6822
@@ -240,7 +240,7 @@ biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.27.8.dist-info/METADATA,sha256=3rTtE5ECOr8Y67BOOCAfleIqkVabeEstjmhzKwxUI-w,882
-biopipen-0.27.8.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.27.8.dist-info/entry_points.txt,sha256=wu70aoBcv1UahVbB_5237MY-9M9_mzqmWjDD-oi3yz0,621
-biopipen-0.27.8.dist-info/RECORD,,
+biopipen-0.27.9.dist-info/METADATA,sha256=-Uvdu_dbpiM0EPBLSFLhhpySPAPxGtA6_FjRlMo0bME,882
+biopipen-0.27.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.27.9.dist-info/entry_points.txt,sha256=wu70aoBcv1UahVbB_5237MY-9M9_mzqmWjDD-oi3yz0,621
+biopipen-0.27.9.dist-info/RECORD,,