biopipen 0.23.0__py3-none-any.whl → 0.23.2__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.23.0"
+__version__ = "0.23.2"

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))$p.value, error = function(e) NA)
                     )
                 )
             test_results <- rbind(test_results, dat)
@@ -390,20 +402,20 @@ add_case_report = function(info, breakdown, test) {
                 )
             ))
         )
-    }
-    if (!is.null(test) && test != "none") {
-        report = c(
-            report,
-            list(list(
-                name = "Tests",
-                contents = list(
-                    list(
-                        kind = "table",
-                        src = file.path(info$casedir, "tests.txt")
+        if (!is.null(test) && test != "none") {
+            report = c(
+                report,
+                list(list(
+                    name = "Tests",
+                    contents = list(
+                        list(
+                            kind = "table",
+                            src = file.path(info$casedir, "tests.txt")
+                        )
                     )
-                )
-            ))
-        )
+                ))
+            )
+        }
     }
     report$h1 = ifelse(
         info$section == "DEFAULT",
@@ -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-0.23.0.dist-info → biopipen-0.23.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.23.0
+Version: 0.23.2
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.23.0.dist-info → biopipen-0.23.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=6bYcjtcATvc99ZNMjTUfPlrJP3-1WenVEc656roVn_I,23
+biopipen/__init__.py,sha256=yninyH3Qwkx3xw1ShRaTmjGR_Q-bmMjaMjZVzxS2tLM,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=Rn7Cta7WsMtmQkKGC4h9d5dU_STaIVBgR8UliiGgL6o,1757
@@ -122,7 +122,7 @@ biopipen/scripts/scrna/ExprImpution.R,sha256=7768ezrr59xUZDXq8lO9jj2XhnkSsx-xxBm
 biopipen/scripts/scrna/MarkersFinder.R,sha256=P0tUurKdEhT-ED49f_c9pqAjQafYiYGE4LJehWblBlQ,26182
 biopipen/scripts/scrna/MetaMarkers.R,sha256=dJJs9fTYNcWJpDs_m_Gu4Z8vYHuTS1ZuORrw5BtXFzY,12348
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=JSHd-_-KiFqW8avCGxgU4T-C5BtDr2u0kwIvEu2lFIg,4188
-biopipen/scripts/scrna/RadarPlots.R,sha256=10u2ltVpjgX5uh6jvEMMxWxqVmZyWNidzyXqD0OYp9k,13439
+biopipen/scripts/scrna/RadarPlots.R,sha256=aYx6eGdvfXCJA7GfryWiCdRHMF6Do8DbO1XzU845sg8,14193
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
 biopipen/scripts/scrna/ScFGSEA.R,sha256=2nJN1AAe55SyR-jwVj5ds2pyt32fTIn548zjvEB4Jt0,7332
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=pZKv1SnSNEGXDeE0_2VYp0GAikYitohW2FR5YGKjs8Q,2351
@@ -218,7 +218,7 @@ biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=bKduqOQjSC8BtZJuwfUShR49omoEMbB57n3Gi6dYlqA,4147
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.23.0.dist-info/METADATA,sha256=3bXDmKUcrul5hdrY8AfOoLobYX7uODE_OePqboxrsF0,886
-biopipen-0.23.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-biopipen-0.23.0.dist-info/entry_points.txt,sha256=16Apdku3RFwghe1nb0JR7eVo4IzLae6hCWjU1VxYUn0,525
-biopipen-0.23.0.dist-info/RECORD,,
+biopipen-0.23.2.dist-info/METADATA,sha256=DUY229wIE-gE3ifKTbpHQBjxSNXZAyzRjZTSL4X6gcI,886
+biopipen-0.23.2.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+biopipen-0.23.2.dist-info/entry_points.txt,sha256=16Apdku3RFwghe1nb0JR7eVo4IzLae6hCWjU1VxYUn0,525
+biopipen-0.23.2.dist-info/RECORD,,