Update deprecated igraph for 2.1, #69 #70

cole-trapnell-lab · Jan 3, 2025 · ad3e1f7 · ad3e1f7
1 parent 4af0968
commit ad3e1f7
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Showing 11 changed files with 98 additions and 91 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: garnett
 Type: Package
 Title: Automated cell type classification
-Version: 0.1.23
+Version: 0.1.24
 Author: c(
     person("Hannah", "Pliner", email = "hpliner@uw.edu", role = c("aut", "cre")), 
     person("Cole", "Trapnell", email = "coletrap@uw.edu", role = c("aut")))

diff --git a/R/classify_cells.R b/R/classify_cells.R
@@ -234,7 +234,7 @@ run_classifier <- function(classifier,
   for (v in igraph::V(classifier@classification_tree)){
 
     child_cell_types <- igraph::V(classifier@classification_tree)[
-      suppressWarnings(outnei(v))]$name
+      suppressWarnings(.outnei(v))]$name
 
     if (length(child_cell_types) > 0){
       new_gate_res <- make_predictions(cds, classifier, v,
@@ -258,7 +258,7 @@ run_classifier <- function(classifier,
                                   imputed_gate_res, level_table){
 
     for (child in igraph::V(classifier@classification_tree)[
-      suppressWarnings(outnei(v))]){
+      suppressWarnings(.outnei(v))]){
       curr_level <- paste0("level", tree_levels[child])
       if(!curr_level %in% names(level_table)) {
         level_table[[curr_level]] <- "Unknown"
@@ -362,7 +362,7 @@ make_predictions <- function(cds,
   predictions <- tryCatch({
     if(is.null(cvfit)) {
       child_cell_types <- igraph::V(classifier@classification_tree)[
-        suppressWarnings(outnei(curr_node)) ]$name
+        suppressWarnings(.outnei(curr_node)) ]$name
       predictions <- matrix(FALSE, nrow=nrow(pData(cds)),
                             ncol=length(child_cell_types),
                             dimnames=list(row.names(pData(cds)),

diff --git a/R/get_training_sample.R b/R/get_training_sample.R
@@ -16,7 +16,7 @@ get_training_sample <- function(cds,
   ##### Find type assignment from expressed/not expressed #####
 
   child_cell_types <- igraph::V(classifier@classification_tree)[
-    suppressWarnings(outnei(curr_node)) ]$name
+    suppressWarnings(.outnei(curr_node)) ]$name
   parent <- igraph::V(classifier@classification_tree)[curr_node]$name
   if (length(child_cell_types) > 0) {
     if (length(intersect(child_cell_types,

diff --git a/R/train_cell_classifier.R b/R/train_cell_classifier.R
@@ -284,7 +284,7 @@ train_cell_classifier <- function(cds,
 
   for (v in igraph::V(classifier@classification_tree)){
     child_cell_types <- igraph::V(classifier@classification_tree)[
-      suppressWarnings(outnei(v))]$name
+      suppressWarnings(.outnei(v))]$name
 
     if(length(child_cell_types) > 0) {
       ### Get CDS subset for training ###
@@ -297,7 +297,7 @@ train_cell_classifier <- function(cds,
           make_predictions(norm_cds,
                            classifier,
                            igraph::V(classifier@classification_tree)[
-                             suppressWarnings(innei(v))]$name,
+                             suppressWarnings(.innei(v))]$name,
                            rank_prob_ratio = 1.1,
                            s = "lambda.min")
         if(!igraph::V(classifier@classification_tree)[v]$name %in%
@@ -557,7 +557,7 @@ propogate_func <- function(curr_node,
                            parse_list,
                            classifier) {
   children <- igraph::V(classifier@classification_tree)[
-    suppressWarnings(outnei(curr_node))]$name
+    suppressWarnings(.outnei(curr_node))]$name
 
   if(length(children) == 0) {
     return(parse_list[[curr_node]]@expressed)

diff --git a/R/utils.R b/R/utils.R
@@ -403,7 +403,7 @@ check_markers <- function(cds,
   ##### For each node #####
   for (v in igraph::V(classifier@classification_tree)){
     child_cell_types <-
-      igraph::V(classifier@classification_tree)[suppressWarnings(outnei(v))]$name
+      igraph::V(classifier@classification_tree)[suppressWarnings(.outnei(v))]$name
 
     if(length(child_cell_types) == 0) next
 

diff --git a/garnett.Rproj b/garnett.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 1f11074e-b3a3-45d7-991d-16847e3f34b1
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

diff --git a/tests/testthat/_snaps/utils/basic-marker-plot-change-amb.svg b/tests/testthat/_snaps/utils/basic-marker-plot-change-amb.svg