Update pbmc_small to latest v3 standards

ws2260 · Apr 15, 2019 · 209717b · 209717b
1 parent f96309a
commit 209717b
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Showing 10 changed files with 16 additions and 16 deletions.
diff --git a/R/visualization.R b/R/visualization.R
@@ -418,7 +418,7 @@ HTOHeatmap <- function(
 #' @export
 #'
 #' @examples
-#' RidgePlot(object = pbmc_small, features = 'PC1')
+#' RidgePlot(object = pbmc_small, features = 'PC_1')
 #'
 RidgePlot <- function(
   object,
@@ -473,7 +473,7 @@ RidgePlot <- function(
 #' @seealso \code{\link{FetchData}}
 #'
 #' @examples
-#' VlnPlot(object = pbmc_small, features = 'PC1')
+#' VlnPlot(object = pbmc_small, features = 'PC_1')
 #' VlnPlot(object = pbmc_small, features = 'LYZ', split.by = 'groups')
 #'
 VlnPlot <- function(
@@ -694,7 +694,7 @@ DimPlot <- function(
 #'     \item An \code{Assay} feature (e.g. a gene name - "MS4A1")
 #'     \item A column name from meta.data (e.g. mitochondrial percentage - "percent.mito")
 #'     \item A column name from a \code{DimReduc} object corresponding to the cell embedding values
-#'     (e.g. the PC1 scores - "PC_1")
+#'     (e.g. the PC 1 scores - "PC_1")
 #' }
 #' @param cols The two colors to form the gradient over. Provide as string vector with
 #' the first color corresponding to low values, the second to high. Also accepts a Brewer
@@ -730,7 +730,7 @@ DimPlot <- function(
 #' \code{\link{CellSelector}}
 #'
 #' @examples
-#' FeaturePlot(object = pbmc_small, features = 'PC1')
+#' FeaturePlot(object = pbmc_small, features = 'PC_1')
 #'
 FeaturePlot <- function(
   object,

diff --git a/data/pbmc_small.rda b/data/pbmc_small.rda
diff --git a/man/FeaturePlot.Rd b/man/FeaturePlot.Rd
diff --git a/man/FetchData.Rd b/man/FetchData.Rd
diff --git a/man/OldWhichCells.Rd b/man/OldWhichCells.Rd
diff --git a/man/PolyFeaturePlot.Rd b/man/PolyFeaturePlot.Rd
diff --git a/man/RidgePlot.Rd b/man/RidgePlot.Rd
diff --git a/man/SubsetData.Rd b/man/SubsetData.Rd
diff --git a/man/VlnPlot.Rd b/man/VlnPlot.Rd
diff --git a/tests/testthat/test_objects.R b/tests/testthat/test_objects.R
@@ -222,13 +222,13 @@ Key(pbmc_small[["RNA2"]]) <- "rna2_"
 test_that("Fetching keyed variables works", {
   x <- FetchData(object = pbmc_small, vars = c(paste0("rna_", rownames(x = pbmc_small)[1:5]), paste0("rna2_", rownames(x = pbmc_small)[1:5])))
   expect_equal(colnames(x = x), c(paste0("rna_", rownames(x = pbmc_small)[1:5]), paste0("rna2_", rownames(x = pbmc_small)[1:5])))
-  x <- FetchData(object = pbmc_small, vars = c(paste0("rna_", rownames(x = pbmc_small)[1:5]), paste0("PC", 1:5)))
-  expect_equal(colnames(x = x), c(paste0("rna_", rownames(x = pbmc_small)[1:5]), paste0("PC", 1:5)))
+  x <- FetchData(object = pbmc_small, vars = c(paste0("rna_", rownames(x = pbmc_small)[1:5]), paste0("PC_", 1:5)))
+  expect_equal(colnames(x = x), c(paste0("rna_", rownames(x = pbmc_small)[1:5]), paste0("PC_", 1:5)))
 })
 
 test_that("Fetching embeddings/loadings not present returns warning or errors", {
-  expect_warning(FetchData(object = pbmc_small, vars = c("PC1", "PC100")))
-  expect_error(FetchData(object = pbmc_small, vars = "PC100"))
+  expect_warning(FetchData(object = pbmc_small, vars = c("PC_1", "PC_100")))
+  expect_error(FetchData(object = pbmc_small, vars = "PC_100"))
 })
 
 bad.gene <- GetAssayData(object = pbmc_small[["RNA"]], slot = "data")