Mercurial > repos > ethevenot > qualitymetrics
diff qualitymetrics_script.R @ 1:6d3b7b6573d8 draft
planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7
| author | ethevenot |
|---|---|
| date | Fri, 21 Oct 2016 12:56:22 -0400 |
| parents | b4f5b5bc01dd |
| children | 596320b84315 |
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--- a/qualitymetrics_script.R Sat Aug 06 12:01:17 2016 -0400 +++ b/qualitymetrics_script.R Fri Oct 21 12:56:22 2016 -0400 @@ -424,14 +424,16 @@ text(1, 0.45, adj=0, cex = 1.1, labels = paste0("mean: ", signif(mean(datMN, na.rm=TRUE), 2))) text(1, 0.35, adj=0, cex = 1.1, labels = paste0("max: ", signif(max(datMN, na.rm=TRUE), 2))) if("sampleType" %in% colnames(samDF) && - "pool" %in% samDF[, "sampleType"]) + "pool" %in% samDF[, "sampleType"]) { + poolCvNanVl <- is.nan(varDF[, "pool_CV"]) text(1, 0.25, adj=0, cex = 1.1, labels = paste0("pool CV < ", round(thrVn["poolCv"] * 100), "%: ", - round(sum(varDF[, "pool_CV"] < thrVn["poolCv"]) / nrow(varDF) * 100), + round(sum(varDF[!poolCvNanVl, "pool_CV", drop = FALSE] < thrVn["poolCv"]) / nrow(varDF) * 100), "%")) + } text(1, 0.1, adj=0, labels = paste0("Thresholds used in plots:")) text(1, 0, adj=0, labels = paste0(" p-value = ", thrVn["pvalue"]))