Mercurial > repos > iuc > limma_voom
changeset 22:708348a17fa1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8c4b8f8711df0a4d6fa98fa8a6f91b977395d62c"
| author | iuc |
|---|---|
| date | Sat, 26 Jun 2021 19:10:16 +0000 |
| parents | 58c35179ebf0 |
| children | e827f9aae031 |
| files | limma_voom.R limma_voom.xml |
| diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/limma_voom.R Fri Jun 04 20:37:04 2021 +0000 +++ b/limma_voom.R Sat Jun 26 19:10:16 2021 +0000 @@ -316,7 +316,7 @@ # Process factors if (is.null(opt$factInput)) { - factordata <- read.table(opt$factFile, header = TRUE, sep = "\t", strip.white = TRUE) + factordata <- read.table(opt$factFile, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = TRUE) if (!setequal(factordata[, 1], colnames(counts))) stop("Sample IDs in counts and factors files don't match") # order samples as in counts matrix @@ -345,7 +345,7 @@ } # make groups valid R names, required for makeContrasts factors <- sapply(factors, make.names) -factors <- data.frame(factors) +factors <- data.frame(factors, stringsAsFactors = TRUE) # if annotation file provided if (have_anno) { @@ -475,15 +475,16 @@ } else if (filt_smpcount) { keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq } else if (filt_cpm) { - - keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq + cpms <- cpm(data$counts) + thresh <- cpms >= opt$cpmReq + keep <- rowSums(thresh) >= opt$sampleReq if ("c" %in% plots) { # Plot CPM vs raw counts (to check threshold) pdf(cpm_pdf, width = 6.5, height = 10) par(mfrow = c(3, 2)) for (i in seq_len(nsamples)) { - plot(data$counts[, i], myCPM[, i], xlim = c(0, 50), ylim = c(0, 3), main = samplenames[i], xlab = "Raw counts", ylab = "CPM") + plot(data$counts[, i], cpms[, i], xlim = c(0, 50), ylim = c(0, 3), main = samplenames[i], xlab = "Raw counts", ylab = "CPM") abline(v = 10, col = "red", lty = 2, lwd = 2) abline(h = opt$cpmReq, col = 4) } @@ -672,7 +673,6 @@ a1 <- suppressWarnings(cmdscale(as.dist(dd), k = min(ndim, 8), eig = TRUE)) eigen <- data.frame(name = 1:min(ndim, 8), eigen = round(a1$eig[1:min(ndim, 8)] / sum(a1$eig), 2)) - png(mdsscree_png, width = 1000, height = 500) par(mfrow = c(1, 2)) plotMDS(y, labels = samplenames, col = as.numeric(factors[, 1]), main = "MDS Plot: Dims 1 and 2")
--- a/limma_voom.xml Fri Jun 04 20:37:04 2021 +0000 +++ b/limma_voom.xml Sat Jun 26 19:10:16 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="limma_voom" name="limma" version="3.48.0"> +<tool id="limma_voom" name="limma" version="3.48.0+galaxy1"> <description> Perform differential expression with limma-voom or limma-trend </description>