biopipen 0.22.7__py3-none-any.whl → 0.22.8__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.22.7"
+__version__ = "0.22.8"

biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R

@@ -159,7 +159,7 @@ do_one_group <- function(group) {
     }
 }
 
-groups = as.character(unique(sobj@meta.data[[grouping]]))
+groups = sort(as.character(unique(sobj@meta.data[[grouping]])))
 if (ncores == 1) {
     lapply(groups, do_one_group)
 } else {

biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R

@@ -203,7 +203,7 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
             pvalues_mat[p, c] <- pval
         }
     }
-    all_NA <- rowAlls(is.na(mean_expression_shuffle))
+    all_NA <- rowAlls(is.na(mean_expression_shuffle), useNames = F)
     mean_expression_shuffle <- mean_expression_shuffle[!all_NA, , drop = F]
     # heatmap
     dat <- mean_expression_shuffle
@@ -212,7 +212,7 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
     sort_column <- c()
 
     for (i in colnames(dat)) {
-        select_row <- which(rowMaxs(dat, na.rm = T) == dat[, i])
+        select_row <- which(rowMaxs(dat, na.rm = T, useNames = F) == dat[, i])
         tmp <- rownames(dat)[select_row][order(dat[select_row, i], decreasing = T)]
         sort_row <- c(sort_row, tmp)
     }
@@ -282,7 +282,7 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
         args = list(
             mapping = aes(x = variable, y = value, fill = variable),
             trim = F,
-            size = 0.2,
+            linewidth = 0.2,
             show.legend = F,
             width = 1.2
         ),
@@ -357,7 +357,7 @@ do_one_subset_col <- function(subset_col, subset_prefix) {
                     row_names_max_width = max_text_width(pws, gp = gpar(fontsize = 12)),
                     row_dend_reorder = TRUE,
                     row_dend_width = unit(30, "mm"),
-                    column_split = do_call(c, lapply(1:length(subsets), function(i) {rep(subsets[i], ncol(x[[i]]$hmdata))})),
+                    column_split = unlist(lapply(1:length(subsets), function(i) {rep(subsets[i], ncol(x[[i]]$hmdata))})),
                     cluster_columns = FALSE
                 ),
                 devpars = hm_devpars,

biopipen/utils/gsea.R

@@ -14,8 +14,8 @@ prerank = function(
     # See: https://gseapy.readthedocs.io/en/latest/_modules/gseapy/algorithm.html#ranking_metric
     expr_pos_mean = rowMeans(exprdata[, classes == pos, drop=F], na.rm=TRUE)
     expr_neg_mean = rowMeans(exprdata[, classes == neg, drop=F], na.rm=TRUE)
-    expr_pos_std = rowSds(as.matrix(exprdata[, classes == pos, drop=F]), na.rm=TRUE)
-    expr_neg_std = rowSds(as.matrix(exprdata[, classes == neg, drop=F]), na.rm=TRUE)
+    expr_pos_std = rowSds(as.matrix(exprdata[, classes == pos, drop=F]), na.rm=TRUE, useNames = T)
+    expr_neg_std = rowSds(as.matrix(exprdata[, classes == neg, drop=F]), na.rm=TRUE, useNames = T)
     rands = rnorm(length(expr_neg_std)) * 1e-6
 
     if (method %in% c("s2n", "signal_to_noise")) {

{biopipen-0.22.7.dist-info → biopipen-0.22.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.22.7
+Version: 0.22.8
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.22.7.dist-info → biopipen-0.22.8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=A-PCmnFCMZxIhCv-dXpG9uKeIOhjJzgJKVRpj3pY5Ys,23
+biopipen/__init__.py,sha256=EOysPoftuC2obWtC-OXdrP2U1GFGj8atmVYzLWnwLuI,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
@@ -145,8 +145,8 @@ biopipen/scripts/scrna/TopExpressingGenes.R,sha256=ZTmk09LNwrZfVLbjDZ1QJbLAvA4GS
 biopipen/scripts/scrna/Write10X.R,sha256=EHefujCvOuSTBRtPUVmzJFKo2I7M2zPWDbbmPWmqdxo,284
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
 biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=zB-nOsC8P0cOv1hcqgXOciGSJ5i3QfLTpIds7XkwaLQ,3893
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=SJMLumGOjt8ZotlmHfzzveJEE4hpvUk5kyT892pDxHs,4887
-biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=8mPntv1WDJuryn3jON72xD6ZWHToa7g6Je4A3cF_sUI,15876
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=gWAzdtaC_o8P9WHVQ7-5Tg8XNv6D-OiSU7dKcEJMWr8,4893
+biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=qEcRuONt4Ijm6ysoPqGgOk46klAQwgVbQhnwHfXRknI,15905
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=PcLv40S1lbdaTKzCDis1iVLABCFSRwKyajA_62O87lo,9733
 biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-PWY03hc,704
 biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
@@ -208,7 +208,7 @@ biopipen/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/utils/common_docstrs.py,sha256=7mAXf7bE2Px4xWifOKGAilkcFdc1C-xKnglQR1oTqw4,3885
 biopipen/utils/gene.R,sha256=BzAwlLA8hO12vF-3t6IwEuTEeLa_jBll4zm_5qe3qoE,1243
 biopipen/utils/gene.py,sha256=qE_BqTayrJWxRdniffhcz6OhZcw9GUoOrj2EtFWH9Gw,2246
-biopipen/utils/gsea.R,sha256=o3RC-wejsfFXPXzRIpFw22F-aif27qnuKEPavvXIlkc,5794
+biopipen/utils/gsea.R,sha256=KsSWNoRwPsSsWfNS2Iu5qKi9QQYsqn47wARm0QgV68w,5822
 biopipen/utils/io.R,sha256=jIYdqdn0iRWfQYAZa5CjXi3fikqmYvPPLIXhobRe8sw,537
 biopipen/utils/misc.R,sha256=nkjiAsEsilq0AeiKRDNqrhTx-1Grqg-rFlkjOEOEDYg,5224
 biopipen/utils/misc.py,sha256=Pmh3CBiKJ3vC_RqorfOfRAvTVKXrGDJT8DMLfYbTivs,3055
@@ -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-0.22.7.dist-info/METADATA,sha256=_CWuhaUCCrcSTT1jpHYKLlDqHqYnhFjMgCrSCBjIsUk,886
-biopipen-0.22.7.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-biopipen-0.22.7.dist-info/entry_points.txt,sha256=-rKo4gInvzqlh7_2oEVmEo9gKO9y1ba3rHWTWOM5xP4,561
-biopipen-0.22.7.dist-info/RECORD,,
+biopipen-0.22.8.dist-info/METADATA,sha256=qmO4X3KbCYvYAf7NHiIyljm3OyA80id21GTjpI_tr28,886
+biopipen-0.22.8.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+biopipen-0.22.8.dist-info/entry_points.txt,sha256=-rKo4gInvzqlh7_2oEVmEo9gKO9y1ba3rHWTWOM5xP4,561
+biopipen-0.22.8.dist-info/RECORD,,