biopipen 0.23.1__tar.gz → 0.23.3__tar.gz

{biopipen-0.23.1 → biopipen-0.23.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.23.1
+Version: 0.23.3
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.23.3/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.23.3"

{biopipen-0.23.1 → biopipen-0.23.3}/biopipen/ns/tcr.py

@@ -87,7 +87,7 @@ class ImmunarchLoading(Proc):
     envs = {
         "tmpdir": config.path.tmpdir,
         "prefix": "{Sample}_",
-        "mode": "single",
+        "mode": "paired",
         "extracols": [],
     }
     script = "file://../scripts/tcr/ImmunarchLoading.R"

{biopipen-0.23.1 → biopipen-0.23.3}/biopipen/scripts/scrna/RadarPlots.R

@@ -294,6 +294,7 @@ do_barplot_and_tests <- function(info, case, counts) {
         geom_errorbar(
             aes(ymin = mean_sd1, ymax = mean_sd2),
             width = 0.4,
+            linewidth = 0.8,
             position = position_dodge(0.9),
             color = "#333333"
         ) +
@@ -326,10 +327,21 @@ do_barplot_and_tests <- function(info, case, counts) {
                 group_by(!!sym(case$ident)) %>%
                 summarise(
                     comparison = paste0(pair, collapse = " - "),
+                    n = paste(as.list(table(!!sym(case$by)))[pair], collapse = "; "),
+                    mean = paste(
+                        (tibble(.frac, !!sym(case$by)) %>%
+                            group_by(!!sym(case$by)) %>%
+                            summarise(mean = mean(.frac)) %>%
+                            column_to_rownames(case$by) %>%
+                            t() %>%
+                            as.data.frame() %>%
+                            as.list())[pair] %>% unlist() %>% round(3),
+                        collapse = "; "
+                    ),
                     !!sym(paste0(case$test, "_pval")) := ifelse(
                         case$test == "wilcox",
-                        wilcox.test(.frac ~ !!sym(case$by))$p.value,
-                        t.test(.frac ~ !!sym(case$by))$p.value
+                        tryCatch(wilcox.test(.frac ~ !!sym(case$by))$p.value, error = function(e) NA),
+                        tryCatch(t.test(.frac ~ !!sym(case$by))$p.value, error = function(e) NA)
                     )
                 )
             test_results <- rbind(test_results, dat)
@@ -426,10 +438,11 @@ run_one_case <- function(casename) {
 
     # Get the counts
     if (!is.null(case$each)) {
-        counts <- meta %>% filter(!!sym(case$each) == case$each_value) %>% drop_na(!!sym(case$by))
+        counts <- meta %>% filter(!!sym(case$each) == case$each_value)
     } else {
-        counts <- meta %>% drop_na(!!sym(case$by))
+        counts <- meta
     }
+    counts <- counts %>% drop_na(!!sym(case$by)) %>% drop_na(!!sym(case$ident))
     do_radarplot(info, case, counts)
 
     if (!is.null(case$breakdown)) {

{biopipen-0.23.1 → biopipen-0.23.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.23.1"
+version = "0.23.3"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.23.1 → biopipen-0.23.3}/setup.py

@@ -75,7 +75,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.23.1',
+    'version': '0.23.3',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.23.1/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.23.1"