change argument names for iSEEinit

NajlaAbassi · Mar 21, 2024 · a5f0ecb · a5f0ecb
1 parent 1a56857
commit a5f0ecb
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Showing 7 changed files with 23 additions and 22 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -40,7 +40,7 @@
 #' cluster <- "stimulus"
 #' group <- "single cell quality"
 #' initial <- iSEEinit(sce = sce,
-#'                     feature.list = gene_list,
+#'                     features = gene_list,
 #'                     clusters = cluster,
 #'                     groups = group)
 #'
@@ -183,7 +183,7 @@ view_initial_tiles <- function(initial) {
 #' cluster <- "stimulus"
 #' group <- "single cell quality"
 #' initial <- iSEEinit(sce = sce,
-#'                     feature.list = gene_list,
+#'                     features = gene_list,
 #'                     clusters = cluster,
 #'                     groups = group)
 #'
@@ -302,11 +302,11 @@ view_initial_network <- function(initial,
 #' cluster <- "stimulus"
 #' group <- "single cell quality"
 #' initial1 <- iSEEinit(sce = sce,
-#'                      feature.list = gene_list_1,
+#'                      features = gene_list_1,
 #'                      clusters = cluster,
 #'                      groups = group)
 #' initial2 <- iSEEinit(sce = sce,
-#'                      feature.list = gene_list_2,
+#'                      features = gene_list_2,
 #'                      clusters = cluster,
 #'                      groups = group)
 #' initials_merged <- glue_initials(initial1,

diff --git a/README.md b/README.md
@@ -47,7 +47,7 @@ gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437")
 cluster <- "stimulus"
 group <- "single cell quality"
 
-initial <- iSEEinit(sce = sce, feature.list = gene_list, clusters = cluster, groups = group)
+initial <- iSEEinit(sce = sce, features = gene_list, clusters = cluster, groups = group)
 
 iSEE(sce, initial = initial)
 ```

diff --git a/man/glue_initials.Rd b/man/glue_initials.Rd
diff --git a/man/iSEEinit.Rd b/man/iSEEinit.Rd
diff --git a/man/view_initial_network.Rd b/man/view_initial_network.Rd
diff --git a/man/view_initial_tiles.Rd b/man/view_initial_tiles.Rd
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -1,15 +1,16 @@
 test_that("iSEEfier utils work", {
   init_1 <- iSEEinit(sce = sce_allen,
-                      feature.list = c("Il2rb",
+                      features = c("Il2rb",
                                        "Klre1"),
                       clusters = "Primary.Type",
                       groups = "Secondary.Type")
   expect_true(is.list(init_1))
 
   init_2 <- iSEEinit(sce = sce_allen,
-                     feature.list = c("Actb", "Gapdh"),
+                     features = c("Actb", "Gapdh"),
                      clusters = "Primary.Type",
-                     groups = "Secondary.Type", markdownboard = TRUE)
+                     groups = "Secondary.Type",
+                     add_markdown_panel = TRUE)
   expect_true(is.list(init_2))
 
   expect_true(length(init_1) == 10)