| Previous changeset 8:342570ad880c (2018-08-04) Next changeset 10:9a52306991b3 (2018-09-01) |
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Commit message:
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 |
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modified:
w4mcorcov.xml w4mcorcov_lib.R w4mcorcov_salience.R w4mcorcov_wrapper.R |
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| diff -r 342570ad880c -r 06c51af11531 w4mcorcov.xml --- a/w4mcorcov.xml Sat Aug 04 17:43:16 2018 -0400 +++ b/w4mcorcov.xml Fri Aug 10 11:15:31 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-\xef\xbb\xbf<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.12">\n+\xef\xbb\xbf<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.13">\n <description>OPLS-DA Contrasts of Univariate Results</description>\n <macros>\n <xml name="paramPairSigFeatOnly">\n@@ -20,8 +20,14 @@\n </xml>\n </macros>\n <requirements>\n+ <!--\n+ <requirement type="package" version="3.4.1">r-base</requirement>\n+ <requirement type="package" version="1.1_4">r-batch</requirement>\n+ <requirement type="package" version="1.2.14">bioconductor-ropls</requirement>\n+ -->\n+ <requirement type="package">r-base</requirement>\n <requirement type="package">r-batch</requirement>\n- <requirement type="package">bioconductor-ropls</requirement>\n+ <requirement type="package" version="1.10.0">bioconductor-ropls</requirement>\n </requirements>\n <command detect_errors="aggressive"><![CDATA[\n Rscript \'$__tool_directory__/w4mcorcov_wrapper.R\'\n@@ -54,13 +60,12 @@\n ]]></command>\n \n <inputs>\n- <param name="dataMatrix_in" type="data" format="tabular" label="Data matrix file"\n- help="Features x samples (tabular data - decimal: \'.\'; missing: NA; mode: numerical; separator: tab character)" />\n- <param name="sampleMetadata_in" type="data" format="tabular" label="Sample metadata file"\n- help="Samples x metadata (tabular data - decimal: \'.\'; missing: NA; mode: character or numerical; separator: tab character)" />\n- <param name="variableMetadata_in" type="data" format="tabular"\n- label="Variable metadata file (ideally from Univariate)"\n- help="Features x metadata (tabular data - decimal: \'.\'; missing: NA; mode: character or numerical; separator: tab character)" />\n+ <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"\n+ help="variables ✖ samples" />\n+ <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"\n+ help="sample metadata, one row per sample" />\n+ <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)"\n+ type="data" help="variable metadata, one row per variable" />\n <param name="facC" type="text"\n label="Factor of interest"\n help="REQUIRED - The name of the column of sampleMetadata corresponding to the qualitative variable used to define the contrasts. Except when the \'Univariate Significance-test\' is set to \'none\', this also must be a portion of the column names in the variableMetadata file."/>\n@@ -149,7 +154,7 @@\n * Wiklund_2008 covariance\n * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p]\n * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o]\n- * (When filtering on significance of univariate tests) Significance of test of null hypothesis that there is no difference between the two classes, i.e, the pair-wise test.\n+ * When filtering on significance of univariate tests,significance of test of null hypothesis that there is no difference between the two classes, i.e, the pair-wise test.\n -->\n <data name="contrast_corcov" format="tabular" label="${tool.name}_${variableMetadata_in.name}_corcov" />\n <!--\n@@ -424,7 +429,7 @@\n It must be stressed that there may be no *single* definitive computational approach to select features that are reliable biomarkers, especially from a small number of samples or experiments. A few possible choices are:\n \n - picking features with maximum loadings along the projection parallel to the predictor (loadp),\n-- examining extreme values on S-PLOTs (for which covariance is linearly related to loadp),\n+- examining extreme values on S-PLOTs\n - examining "variable importance in projection VIP for OPLS-DA" (Galindo-Prieto *et al.* 2014), and\n - examining a feature\'s "selectivity ratio" (Rajalahti *et al.*'..b'raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_lohi.pdf |\n- +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Input Parameter or Result | Value |\n+ +============================================+==============================================================================================================================================+\n+ | Factor of interest | lohi |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Univariate Significance-Test | none |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Levels of interest | low,high |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Level-name matching | use regular expressions for matching level-names |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Number of features having extreme loadings | 3 |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_lohi.tsv |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_lohi.tsv |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n+ | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_lohi.pdf |\n+ +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+\n \n \n Trademarks\n' |
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| diff -r 342570ad880c -r 06c51af11531 w4mcorcov_lib.R --- a/w4mcorcov_lib.R Sat Aug 04 17:43:16 2018 -0400 +++ b/w4mcorcov_lib.R Fri Aug 10 11:15:31 2018 -0400 |
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| @@ -1,3 +1,12 @@ suppressMessages(library(batch)) # suppressMessages(library(foreach)) suppressMessages(library(ropls)) +suppressMessages(library(methods)) + +# cat("Installed packages:",stderr()) +# write.table((installed.packages(.Library, priority = "high"))[, c(1,3:5)], stderr()) +# cat("Loaded packages:",stderr()) +# write(.packages(), stderr()) + +print(sessionInfo()) + |
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| diff -r 342570ad880c -r 06c51af11531 w4mcorcov_salience.R --- a/w4mcorcov_salience.R Sat Aug 04 17:43:16 2018 -0400 +++ b/w4mcorcov_salience.R Fri Aug 10 11:15:31 2018 -0400 |
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| @@ -61,8 +61,8 @@ ) rcvOfFeatureBySampleClassLevel[is.nan(rcvOfFeatureBySampleClassLevel)] <- max(9999,max(rcvOfFeatureBySampleClassLevel, na.rm = TRUE)) - # "For each feature, 'select max(median_feature_intensity) from feature'." - maxApplyMedianOfFeatureBySampleClassLevel <- sapply( + # "For each feature, 'select max(max_feature_intensity) from feature'." + maxApplyMaxOfFeatureBySampleClassLevel <- sapply( X = 1:n_features , FUN = function(i) { match( @@ -84,19 +84,19 @@ # the feature name feature = features # the name (or factor-level) of the class-level with the highest median intensity for the feature - , max_level = medianOfFeatureBySampleClassLevel[maxApplyMedianOfFeatureBySampleClassLevel,1] + , max_level = medianOfFeatureBySampleClassLevel[maxApplyMaxOfFeatureBySampleClassLevel,1] # the median intensity for the feature and the level max_level , max_median = sapply( X = 1:n_features , FUN = function(i) { - maxOfFeatureBySampleClassLevel[maxApplyMedianOfFeatureBySampleClassLevel[i], 1 + i] + maxOfFeatureBySampleClassLevel[maxApplyMaxOfFeatureBySampleClassLevel[i], 1 + i] } ) # the coefficient of variation (expressed as a proportion) for the intensity for the feature and the level max_level , max_rcv = sapply( X = 1:n_features , FUN = function(i) { - rcvOfFeatureBySampleClassLevel[maxApplyMedianOfFeatureBySampleClassLevel[i], i] + rcvOfFeatureBySampleClassLevel[maxApplyMaxOfFeatureBySampleClassLevel[i], i] } ) # the mean of the medians of intensity for all class-levels for the feature |
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| diff -r 342570ad880c -r 06c51af11531 w4mcorcov_wrapper.R --- a/w4mcorcov_wrapper.R Sat Aug 04 17:43:16 2018 -0400 +++ b/w4mcorcov_wrapper.R Fri Aug 10 11:15:31 2018 -0400 |
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| @@ -55,12 +55,6 @@ source(paste(script.dir, "w4mcorcov_salience.R", sep="/")) source(paste(script.dir, "w4mcorcov_calc.R", sep="/")) source(paste(script.dir, "w4mcorcov_output.R", sep="/")) -#source("w4mcorcov_lib.R") -#source("w4mcorcov_util.R") -#source("w4mcorcov_input.R") -#source("w4mcorcov_salience.R") -#source("w4mcorcov_calc.R") -#source("w4mcorcov_output.R") ## log file ##--------- |