Mercurial > repos > ethevenot > qualitymetrics
changeset 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 |
| files | README.md build.xml qualitymetrics_config.xml qualitymetrics_script.R |
| diffstat | 4 files changed, 22 insertions(+), 8 deletions(-) [+] |
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--- a/README.md Sat Aug 06 12:01:17 2016 -0400 +++ b/README.md Fri Oct 21 12:56:22 2016 -0400 @@ -7,8 +7,8 @@ ### Description -**Version:** 2.2.4 -**Date:** 2016-08-04 +**Version:** 2.2.6 +**Date:** 2016-10-21 **Author:** Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST) **Email:** [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) **Citation:** @@ -52,6 +52,12 @@ ### News +##### CHANGES IN VERSION 2.2.6 + +MINOR MODIFICATION + + * Graphic (pool_CV inferior to 30% metric): pools with a NaN value are now counted as having a value superior to 30% (to avoid generating a final NA metric value) + ##### CHANGES IN VERSION 2.2.4 INTERNAL MODIFICATION
--- a/build.xml Sat Aug 06 12:01:17 2016 -0400 +++ b/build.xml Fri Oct 21 12:56:22 2016 -0400 @@ -36,7 +36,7 @@ <arg value="--conda_prefix"/> <arg value="${conda.dir}"/> <arg value="--galaxy_branch"/> - <arg value="release_16.01"/> + <arg value="release_16.07"/> <arg value="--conda_dependency_resolution"/> <arg value="${tool.xml}"/> </exec>
--- a/qualitymetrics_config.xml Sat Aug 06 12:01:17 2016 -0400 +++ b/qualitymetrics_config.xml Fri Oct 21 12:56:22 2016 -0400 @@ -1,10 +1,10 @@ -<tool id="quality_metrics" name="Quality Metrics" version="2.2.4"> +<tool id="quality_metrics" name="Quality Metrics" version="2.2.6"> <description>Metrics and graphics to check the quality of the data</description> <requirements> - <requirement type="package" version="3.2.2">R</requirement> + <requirement type="package" version="3.3.1">R</requirement> <requirement type="package">r-batch</requirement> - <requirement type="package" version="1.4.2">bioconductor-ropls</requirement> + <requirement type="package">bioconductor-ropls</requirement> </requirements> <stdio> @@ -251,6 +251,12 @@ NEWS ---- +CHANGES IN VERSION 2.2.6 +======================== +MINOR MODIFICATION + +Graphic: pool_CV inferior to 30%: pools with a NaN value are now counted as having a superior to 30% value (to avoid generating an NA metric value) + CHANGES IN VERSION 2.2.4 ========================
--- 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"]))