diff --git a/DESCRIPTION b/DESCRIPTION index 7443922..6b8130e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: rats -Version: 0.6.1 -Date: 2018-02-15 +Version: 0.6.2 +Date: 2018-02-16 Title: Relative Abundance of Transcripts Encoding: UTF-8 Authors: c(person("Kimon Froussios", role=c("aut"), email="k.froussios@dundee.ac.uk"), diff --git a/R/rats.R b/R/rats.R index 11de434..3e5d2bc 100644 --- a/R/rats.R +++ b/R/rats.R @@ -250,7 +250,7 @@ call_DTU <- function(annot= NULL, TARGET_COL= "target_id", PARENT_COL= "parent_i #---------- INTER-REPLICATE VARIABILITY BOOTSTRAP - + if (rboot) { if (verbose) message("Bootstrapping replicates...") @@ -263,6 +263,7 @@ call_DTU <- function(annot= NULL, TARGET_COL= "target_id", PARENT_COL= "parent_i myprogress <- utils::txtProgressBar(min = 0, max = numpairs, initial = 0, char = "=", width = NA, style = 3, file = stderr()) repres <- lapply(1:numpairs, function(p) { # Single-threaded. Forking happens within calculate_DTU(). + # Update progress. if (verbose) setTxtProgressBar(myprogress, p) @@ -270,7 +271,7 @@ call_DTU <- function(annot= NULL, TARGET_COL= "target_id", PARENT_COL= "parent_i # Grab a replicate from each condition. # Scale it up for the number of samples. A.K.A. "what if all my samples were identical and like this one". counts_A <- as.data.table( count_data_A[[ names(count_data_A)[pairs[[p]][1]] ]] ) * resobj$Parameters$num_replic_A - counts_B <- as.data.table( count_data_A[[ names(count_data_B)[pairs[[p]][2]] ]] ) * resobj$Parameters$num_replic_B + counts_B <- as.data.table( count_data_B[[ names(count_data_B)[pairs[[p]][2]] ]] ) * resobj$Parameters$num_replic_B # Do the work. pout <- calculate_DTU(counts_A, counts_B, tx_filter, test_transc, test_genes, "short", abund_thresh, p_thresh, dprop_thresh, correction, threads) diff --git a/R/results.R b/R/results.R index f0b35e4..6e5bcc9 100644 --- a/R/results.R +++ b/R/results.R @@ -547,7 +547,7 @@ plot_overview <- function(dtuo, type="volcano") { #' @param dtuo A DTU object. #' @param type Type of plot. \itemize{ #' \item{"cormat" - Pairwise Pearson's correlation matrix among samples.} -#' +#' } #' @return A ggplot2 object. Simply display it or you can also customize it. #' @import data.table #' @import ggplot2 diff --git a/man/plot_diagnostics.Rd b/man/plot_diagnostics.Rd index 08197a4..f31ae01 100644 --- a/man/plot_diagnostics.Rd +++ b/man/plot_diagnostics.Rd @@ -8,6 +8,10 @@ plot_diagnostics(dtuo, type = "cormat") } \arguments{ \item{dtuo}{A DTU object.} + +\item{type}{Type of plot. \itemize{ + \item{"cormat" - Pairwise Pearson's correlation matrix among samples.} +}} } \value{ A ggplot2 object. Simply display it or you can also customize it.