Merge pull request #48 from omnideconv/devel

Devel branch
omnideconv · Nov 8, 2023 · dcf899e · dcf899e
2 parents 5646b3a + ba47326
commit dcf899e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: SimBu
 Title: Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
-Version: 1.1.5
+Version: 1.5.0
 Authors@R: 
     person(given = "Alexander",
            family = "Dietrich",

diff --git a/R/access_sfaira.R b/R/access_sfaira.R
@@ -248,12 +248,12 @@ download_sfaira_multiple <- function(setup_list, organisms = NULL, tissues = NUL
 #' @return a dataframe with information on each dataset
 #' @export
 #'
-#' @examples 
+#' @examples
 #' \donttest{
-#'   setup_list <- setup_sfaira(basedir=tempdir())
-#'   # all_datasets <- sfaira_overview(setup_list)
+#' setup_list <- setup_sfaira(basedir = tempdir())
+#' # all_datasets <- sfaira_overview(setup_list)
 #' }
-sfaira_overview <- function(setup_list){
+sfaira_overview <- function(setup_list) {
   # create conda environment with sfaira
   proc <- basilisk::basiliskStart(SimBu_env)
   on.exit(basilisk::basiliskStop(proc))

diff --git a/R/dataset.R b/R/dataset.R
@@ -308,7 +308,7 @@ dataset_merge <- function(dataset_list, name = "SimBu_dataset", spike_in_col = N
 #' @export
 #'
 #' @examples
-#' #h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu")
+#' # h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu")
 #' # ds_h5ad <- SimBu::dataset_h5ad(
 #' #  h5ad_file_counts = h5,
 #' #  name = "h5ad_dataset",
@@ -483,8 +483,8 @@ dataset_seurat <- function(seurat_obj, counts_layer, cell_id_col, cell_type_col,
   if (is.null(counts_layer)) {
     stop("You have to provide the name of the layer in the Seurat object that contains count data.")
   }
-  if(!is.null(assay)){
-    message(paste('Changing default assay to', assay))
+  if (!is.null(assay)) {
+    message(paste("Changing default assay to", assay))
     Seurat::DefaultAssay(seurat_obj) <- assay
   }
   active_assay <- Seurat::DefaultAssay(seurat_obj)
@@ -516,7 +516,7 @@ dataset_seurat <- function(seurat_obj, counts_layer, cell_id_col, cell_type_col,
 
   tryCatch(
     {
-      count_matrix <- SeuratObject::LayerData(seurat_obj, layer = 'counts')
+      count_matrix <- SeuratObject::LayerData(seurat_obj, layer = "counts")
     },
     error = function(e) {
       em <- paste("Could not access count matrix from Seurat object (counts): ", e)
@@ -529,7 +529,7 @@ dataset_seurat <- function(seurat_obj, counts_layer, cell_id_col, cell_type_col,
   if (!is.null(tpm_assay)) {
     tryCatch(
       {
-        tpm_matrix <- SeuratObject::LayerData(seurat_obj, layer = 'data')
+        tpm_matrix <- SeuratObject::LayerData(seurat_obj, layer = "data")
       },
       error = function(e) {
         em <- paste("Could not access count matrix from Seurat object (tpm): ", e)

diff --git a/R/simulator.R b/R/simulator.R
@@ -69,7 +69,7 @@ simulate_sample <- function(data,
     } else {
       # how many cells of this type do we need?
       n <- round(total_cells * simulation_vector[x])
-      if(n == 0){
+      if (n == 0) {
         n <- 1
       }
       cells <- dplyr::slice_sample(cells_of_type_x, n = n, replace = TRUE)

diff --git a/README.md b/README.md
@@ -1,4 +1,3 @@
-
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # SimBu
@@ -10,6 +9,7 @@
 [![docs](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://omnideconv.github.io/SimBu)
 [![Codecov test
 coverage](https://codecov.io/gh/omnideconv/SimBu/branch/master/graph/badge.svg)](https://app.codecov.io/gh/omnideconv/SimBu?branch=master)
+
 <!-- badges: end -->
 
 The goal of SimBu is to simulate pseudo-bulk RNAseq datasets with
@@ -20,14 +20,14 @@ RNAseq datasets.
 
 To install the developmental version of the package, run:
 
-``` r
+```r
 install.packages("devtools")
 devtools::install_github("omnideconv/SimBu")
 ```
 
 To install from Bioconductor:
 
-``` r
+```r
 if (!require("BiocManager", quietly = TRUE)) {
   install.packages("BiocManager")
 }
@@ -40,7 +40,7 @@ BiocManager::install("SimBu")
 Create a dataset-object with local data and simulate a pseudo-bulk
 dataset
 
-``` r
+```r
 library(SimBu)
 # use local data to build dataset
 dataset <- dataset(annotation = annotation_dataframe, count_matrix = expression_matrix, name = "test_dataset")

diff --git a/man/dataset_h5ad.Rd b/man/dataset_h5ad.Rd
diff --git a/man/sfaira_overview.Rd b/man/sfaira_overview.Rd
diff --git a/tests/testthat/test_dataset.R b/tests/testthat/test_dataset.R
@@ -73,7 +73,7 @@ test_that("can create dataset from seurat object", {
 # test_that("can load h5ad file with cells in obs and var", {
 #   h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu")
 #   h5_rev <- system.file("extdata", "anndata_rev.h5ad", package = "SimBu")
-# 
+#
 #   testthat::expect_s4_class(SimBu::dataset_h5ad(h5ad_file_counts = h5, name = "h5ad_dataset", cell_id_col = "id", cell_type_col = "group", cells_in_obs = TRUE), "SummarizedExperiment")
 #   testthat::expect_s4_class(SimBu::dataset_h5ad(h5ad_file_counts = h5_rev, name = "h5ad_dataset", cell_id_col = "id", cell_type_col = "group", cells_in_obs = FALSE), "SummarizedExperiment")
 # })

diff --git a/vignettes/simulator_input_output.Rmd b/vignettes/simulator_input_output.Rmd
@@ -93,14 +93,14 @@ As this function uses the `SimBu` python environment to read the h5ad files and
 
 ```{r}
 # example h5ad file, where cell type info is stored in `obs` layer
-#h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu")
-#ds_h5ad <- SimBu::dataset_h5ad(
+# h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu")
+# ds_h5ad <- SimBu::dataset_h5ad(
 #  h5ad_file_counts = h5,
 #  name = "h5ad_dataset",
 #  cell_id_col = 0, # this will use the rownames of the metadata as cell identifiers
 #  cell_type_col = "group", # this will use the 'group' column of the metadata as cell type info
 #  cells_in_obs = TRUE # in case your cell information is stored in the var layer, switch to FALSE
-#) 
+# )
 ```
 
 ## Merging datasets