From a5f0ecb7c1fc346e8be0193bd4b1fef362c08fd2 Mon Sep 17 00:00:00 2001 From: Najla Abassi Date: Thu, 21 Mar 2024 17:56:51 +0100 Subject: [PATCH] change argument names for iSEEinit --- R/utils.R | 8 ++++---- README.md | 2 +- man/glue_initials.Rd | 4 ++-- man/iSEEinit.Rd | 20 ++++++++++---------- man/view_initial_network.Rd | 2 +- man/view_initial_tiles.Rd | 2 +- tests/testthat/test-utils.R | 7 ++++--- 7 files changed, 23 insertions(+), 22 deletions(-) diff --git a/R/utils.R b/R/utils.R index db51ba7..123bd1c 100644 --- 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 index cdd863f..e42a529 100644 --- 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 index b206213..03f4cae 100644 --- a/man/glue_initials.Rd +++ b/man/glue_initials.Rd @@ -62,11 +62,11 @@ gene_list_2 <- c("ENSMUSG00000005087", "ENSMUSG00000015437") 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/man/iSEEinit.Rd b/man/iSEEinit.Rd index fa5e23f..5aad138 100644 --- a/man/iSEEinit.Rd +++ b/man/iSEEinit.Rd @@ -1,33 +1,33 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/iSEEfier.R +% Please edit documentation in R/iSEEinit.R \name{iSEEinit} \alias{iSEEinit} \title{iSEEinit: Create an initial state of an iSEE instance for gene expression visualization} \usage{ iSEEinit( sce, - feature.list, - reddim.type = "TSNE", + features, + reddim_type = "TSNE", clusters = colnames(colData(sce))[1], groups = colnames(colData(sce))[1], - markdownboard = FALSE, - dynamicMarkerTable = FALSE + add_markdown_panel = FALSE, + add_dynamicTable_panel = FALSE ) } \arguments{ \item{sce}{SingleCellExperiment object} -\item{feature.list}{A character vector containing a list of genes} +\item{features}{A character vector containing a list of genes} -\item{reddim.type}{A string vector containing the dimensionality reduction type} +\item{reddim_type}{A string vector containing the dimensionality reduction type} \item{clusters}{A character string containing the name of the clusters/cell-type/state...(as listed in the colData of the sce)} \item{groups}{A character string of the groups/conditions...(as it appears in the colData of the sce)} -\item{markdownboard}{A logical indicating whether or not to include the MarkdownBoard panel in the initial configuration} +\item{add_markdown_panel}{A logical indicating whether or not to include the MarkdownBoard panel in the initial configuration} -\item{dynamicMarkerTable}{A logical indicating whether or not the DynamicMarkerTable and linked panels should be included in the initial configuration} +\item{add_dynamicTable_panel}{A logical indicating whether or not the DynamicMarkerTable and linked panels should be included in the initial configuration} } \value{ A list of "Panel" objects specifying the initial state of iSEE instance @@ -43,5 +43,5 @@ sce <- scater::runTSNE(sce) 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) } diff --git a/man/view_initial_network.Rd b/man/view_initial_network.Rd index 1780285..375fa3d 100644 --- a/man/view_initial_network.Rd +++ b/man/view_initial_network.Rd @@ -45,7 +45,7 @@ gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437") cluster <- "stimulus" group <- "single cell quality" initial <- iSEEinit(sce = sce, - feature.list = gene_list, + features = gene_list, clusters = cluster, groups = group) diff --git a/man/view_initial_tiles.Rd b/man/view_initial_tiles.Rd index c748026..3b2c8a5 100644 --- a/man/view_initial_tiles.Rd +++ b/man/view_initial_tiles.Rd @@ -39,7 +39,7 @@ gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437") cluster <- "stimulus" group <- "single cell quality" initial <- iSEEinit(sce = sce, - feature.list = gene_list, + features = gene_list, clusters = cluster, groups = group) diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R index 97773f8..d2603d5 100644 --- 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)