DTUrtle 1.0.2 - minor changes. (c463ae9a) · Commits · github_fork / DTUrtle

DESCRIPTION

+1 −1

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@ Package: DTUrtle
		Type: Package
		URL: https://github.com/TobiTekath/DTUrtle, https://tobitekath.github.io/DTUrtle
		Title: Differential Transcript Usage analysis of bulk and single-cell RNA-seq data
		Version: 1.0.1
		Version: 1.0.2
		Authors@R: c(person(given = "Tobias", family = "Tekath", role = c("aut", "cre"), email = "tobias.tekath@wwu.de", comment = c(ORCID = "0000-0002-9315-5452")))
		Description: Easily perform and visualize Differential Transcript Usage (DTU) analysis for bulk or single-cell RNA-seq data, utilizing transcript level quantification counts.
		License: GPL (>= 3) + file LICENSE

+4 −0

Original line number	Diff line number	Diff line
		@@ -256,6 +256,7 @@ check_unique_by_partition <- function(df, partitioning, columns=NULL){
		for(part in partitioning){
		dat <- df[part, cols, drop=FALSE]
		cols <- cols[apply(dat, 2, function(x){all(x == x[1])})]
		cols <- cols[!is.na(cols)]
		if(length(cols)==0){
		return(NULL)
		}
		@@ -286,12 +287,15 @@ get_by_partition <- function(df, partitioning, FUN, columns=NULL, simplify=TRUE,
		if(!is.null(columns)){
		assertthat::assert_that(all(columns %in% colnames(df)))
		df <- df[,columns,drop=FALSE]
		factor_columns <- which(sapply(df,is.factor))
		df[,factor_columns,drop=FALSE] <- apply(df[,factor_columns,drop=FALSE], 2, as.character)
		}
		if(!BiocParallel::bpisup(BPPARAM)){
		BiocParallel::bpstart(BPPARAM)
		}
		ret <- BiocParallel::bpaggregate(df, by=list(rep(names(partitioning), lengths(partitioning))), FUN=FUN, simplify=simplify, drop=TRUE, BPPARAM = BPPARAM)
		BiocParallel::bpstop(BPPARAM)
		ret[,factor_columns,drop=FALSE] <- apply(ret[,factor_columns,drop=FALSE], 2, as.factor)
		return(ret)
		}

+4 −0

Original line number	Diff line number	Diff line
		@@ -796,6 +796,10 @@ plot_transcripts_view <- function(dturtle, genes=NULL, gtf, genome, one_to_one=N
		BiocParallel::bpprogressbar(BPPARAM) <- TRUE
		}

		if(!is.null(savepath) && !dir.exists(savepath)){
		dir.create(file.path(savepath), recursive = TRUE)
		}

		message("Creating ", length(valid_genes), " plots:")
		if(!BiocParallel::bpisup(BPPARAM)){
		BiocParallel::bpstart(BPPARAM)