Merge pull request satijalab#164 from satijalab/fix/NoPipesInFeatures

Ensure feature names don't have pipe characters '|'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.0.3.9025
-Date: 2019-08-01
+Version: 3.0.3.9026
+Date: 2019-08-05
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
 Authors@R: c(

R/objects.R

@@ -466,6 +466,25 @@ CreateAssayObject <- function(
       x = rownames(x = data)
     )
   }
+  if (any(grepl(pattern = '|', x = rownames(x = counts), fixed = TRUE)) || any(grepl(pattern = '|', x = rownames(x = data), fixed = TRUE))) {
+    warning(
+      "Feature names cannot have pipe characters ('|'), replacing with dashes ('-')",
+      call. = FALSE,
+      immediate. = TRUE
+    )
+    rownames(x = counts) <- gsub(
+      pattern = '|',
+      replacement = '-',
+      x = rownames(x = counts),
+      fixed = TRUE
+    )
+    rownames(x = data) <- gsub(
+      pattern = '|',
+      replacement = '-',
+      x = rownames(x = data),
+      fixed = TRUE
+    )
+  }
   # Initialize meta.features
   init.meta.features <- data.frame(row.names = rownames(x = data))
   assay <- new(
@@ -1266,7 +1285,7 @@ UpdateSeuratObject <- function(object) {
         Key(object = object[[ko]]) <- UpdateKey(key = Key(object = object[[ko]]))
       }
       # Check feature names
-      message("Ensuring feature names don't have underscores")
+      message("Ensuring feature names don't have underscores or pipes")
       for (assay.name in FilterObjects(object = object, classes.keep = 'Assay')) {
         assay <- object[[assay.name]]
         for (slot in c('counts', 'data', 'scale.data')) {
@@ -1276,18 +1295,36 @@ UpdateSeuratObject <- function(object) {
               replacement = '-',
               x = rownames(x = slot(object = assay, name = slot))
             )
+            rownames(x = slot(object = assay, name = slot)) <- gsub(
+              pattern = '|',
+              replacement = '-',
+              x = rownames(x = slot(object = assay, name = slot)),
+              fixed = TRUE
+            )
           }
         }
         VariableFeatures(object = assay) <- gsub(
           pattern = '_',
           replacement = '-',
           x = VariableFeatures(object = assay)
         )
+        VariableFeatures(object = assay) <- gsub(
+          pattern = '|',
+          replacement = '-',
+          x = VariableFeatures(object = assay),
+          fixed = TRUE
+        )
         rownames(x = slot(object = assay, name = "meta.features")) <-  gsub(
           pattern = '_',
           replacement = '-',
           x = rownames(x = assay[[]])
         )
+        rownames(x = slot(object = assay, name = "meta.features")) <-  gsub(
+          pattern = '|',
+          replacement = '-',
+          x = rownames(x = assay[[]]),
+          fixed = TRUE
+        )
         object[[assay.name]] <- assay
       }
       for (reduc.name in FilterObjects(object = object, classes.keep = 'DimReduc')) {
@@ -1299,6 +1336,12 @@ UpdateSeuratObject <- function(object) {
               replacement = '-',
               x = rownames(x = slot(object = reduc, name = slot))
             )
+            rownames(x = slot(object = reduc, name = slot)) <- gsub(
+              pattern = '_',
+              replacement = '-',
+              x = rownames(x = slot(object = reduc, name = slot)),
+              fixed = TRUE
+            )
           }
         }
         object[[reduc.name]] <- reduc