biopipen 0.22.6__tar.gz → 0.22.8__tar.gz

{biopipen-0.22.6 → biopipen-0.22.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.22.6
+Version: 0.22.8
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.22.8/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.22.8"

{biopipen-0.22.6 → biopipen-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-0.22.6 → biopipen-0.22.8}/biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R

@@ -128,7 +128,7 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
         mean_exp_eachCellType <- AverageExpression(pathway_metabolic_obj)$RNA
 
         # remove genes which are zeros in any celltype to avoid extreme ratio value
-        keep <- rownames(mean_exp_eachCellType)[rowAlls(mean_exp_eachCellType > 0.001)]
+        keep <- rownames(mean_exp_eachCellType)[rowAlls(mean_exp_eachCellType > 0.001, useNames = F)]
         if (length(keep) < 3) next
 
         # using the loweset value to replace zeros for avoiding extreme ratio value
@@ -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-0.22.6 → biopipen-0.22.8}/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-0.22.6 → biopipen-0.22.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.22.6"
+version = "0.22.8"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.22.6 → biopipen-0.22.8}/setup.py

@@ -76,7 +76,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.22.6',
+    'version': '0.22.8',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.22.6/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.22.6"