added code to source diffex_commons.R; added option to download gene...

added code to source diffex_commons.R; added option to download gene information based on the count matrix rownames; cosmetics

sc_workflow/sc_quality_check.R

@@ -15,15 +15,16 @@ suppressMessages(require(docopt))
 
 doc = '
 Quality control and filtering of scRNAseq data
-Usage: sc_quality_check.R [options] <star_counts_matrix> <design>
+Usage: sc_quality_check.R [options] <count_data> <cell_infos>
 
 Options:
 --file_prefix <sample_name>          add prefix to output files if storing output of multiple analysis in one folder [default: ]
+--gene_info <gene_info>    export gene information [default: FALSE]
 '
 
 
 
-# commandArgs <- function(x) c("../segerstolpe_counts.txt", "../segerstolpe_infos.txt")
+# commandArgs <- function(x) c("--gene_info", "TRUE", "counts_matrix.txt", "cell_infos.txt")
 opts = docopt(doc, commandArgs(TRUE))
 
 
@@ -32,6 +33,7 @@ opts = docopt(doc, commandArgs(TRUE))
 #https://www.bioconductor.org/help/workflows/simpleSingleCell/
 devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/core_commons.R")
 devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/bio/diffex_commons.R")
 devtools::source_url("https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v6/common/cp_utils.R")
 load_pack(SingleCellExperiment)
 load_pack(knitr)
@@ -61,9 +63,10 @@ get.cellcycl.phase <- function(x, annot.db){
 
 # HANDLE input data -------------------------------------------------------------------------------
 
-counts_file <- opts$star_counts_matrix
-design_file <- opts$design
+counts_file <- opts$count_data
+cell_infos_file <- opts$cell_infos
 prefix <- opts$file_prefix
+gene_info <- opts$gene_info
 
 countData <- fread(counts_file)
 
@@ -73,13 +76,13 @@ countMatrix <- countData %>%
 countMatrix <- countMatrix[rowSums(countMatrix)>0, ]
 
 
-design <- fread(design_file) %>% as.data.frame()
+cell_infos <- fread(cell_infos_file) %>% as.data.frame()
 
-if (ncol(countMatrix) != nrow(design)) {print("Count matrix and design have different sample numbers")}
+if (ncol(countMatrix) != nrow(cell_infos)) {print("Count matrix and cell_infos have different sample numbers")}
 
 
 # create SingleCellExperiment object:
-sce <- SingleCellExperiment(assays = list(counts=countMatrix), colData = design)
+sce <- SingleCellExperiment(assays = list(counts=countMatrix), colData = cell_infos)
 
 
 rm(countData)
@@ -250,7 +253,7 @@ summary(sce$outlier)
 
 #  log-normalization
 sce <- normalize(sce)
-scater::plotExplanatoryVariables(sce, variables = c(colnames(design)))
+scater::plotExplanatoryVariables(sce, variables = c(colnames(cell_infos)))
 
 
 #' <br><br>
@@ -288,11 +291,11 @@ if (exists("cc.pairs")) {
 
     # export cell cycle data with its actual data...
     data %>% write_tsv(paste(prefix, "cell_cycle_phases.txt", sep = ""))
-    # ...and only the phase as additional batch effect in the design file
-    design %>%
+    # ...and only the phase as additional batch effect in the cell_infos file
+    cell_infos %>%
         left_join(data, by = "cell_id") %>%
         select(-G1, -S, -G2M) %>%
-        write_tsv(paste(prefix, "basic_design_incl_ccp.txt", sep = ""))
+        write_tsv(paste(prefix, "basic_cell_infos_incl_ccp.txt", sep = ""))
 
     # plot data
     cc_plot <- ggplot(data, aes(G1, G2M, color = phase)) +
@@ -307,14 +310,15 @@ if (exists("cc.pairs")) {
 
 
 # if ensembl_gene_ids were provided, information on gene name, description and coordinates will be downloaded from biomaRt
-if (nchar(db) > 0) {
+if (gene_info == TRUE & nchar(db) > 0) {
     mart <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset = guess_mart(rownames(counts(sce))[1]), host = paste0("oct2018.archive.ensembl.org"), path = "/biomart/martservice", archive = FALSE)
     gene_info = biomaRt::getBM(mart = mart, c("ensembl_gene_id", "external_gene_name", "description", "chromosome_name", "start_position", "end_position") ) %>% tbl_df
-} else {
+    gene_info %>% write_tsv("gene_information.txt")
+} else if (gene_info == TRUE & nchar(db) == 0){
     gene_info = data.frame(gene_id = rownames(rowData(sce)))
+    gene_info %>% write_tsv("gene_information.txt")
 }
 
-gene_info %>% write_tsv("gene_information.txt")
 
 colData(sce) %>% as.data.frame() %>% write_tsv("scater_quality_metrics.txt")