Mercurial > repos > galaxyp > mqppep_preproc
diff mqppep_anova_script.Rmd @ 4:5c2beb4eb41c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1
| author | galaxyp |
|---|---|
| date | Tue, 14 Feb 2023 17:37:36 +0000 |
| parents | bae3a23461c9 |
| children |
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--- a/mqppep_anova_script.Rmd Tue Jan 31 22:27:00 2023 +0000 +++ b/mqppep_anova_script.Rmd Tue Feb 14 17:37:36 2023 +0000 @@ -81,7 +81,7 @@ # should correlation among substrates be used (rather than covariance) correlateSubstrates: TRUE # only show covariance among variables having variance > 1 - filterCovVarGT1: TRUE + filterCovVarGT1: FALSE # maximum number of residues to display for ppeps in rownames or columnames ppepTruncN: 10 # maximum number of characters of subgenes to display in rownames or columnames @@ -97,9 +97,6 @@ kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2" # should debugging trace messages be printed? showEnrichedSubstrates: FALSE - # should debugging nb/nbe messages be printed? - printNBMsgs: FALSE - #printNBMsgs: TRUE # should row-scaling be applied to heatmaps: "none" or "row" defaultHeatMapRowScaling: !r c("none", "row")[1] # how missing values be displayed on heat maps: "NA" or " " @@ -115,6 +112,9 @@ # when debugging files are needed, set debugFileBasePath to the path # to the directory where they should be written debugFileBasePath: !r if (TRUE) NULL else "test-data" + # should debugging nb/nbe messages be printed? + printNBMsgs: FALSE + #printNBMsgs: TRUE --- ```{r setup, include = FALSE, results = 'asis'} @@ -6011,7 +6011,7 @@ p_value_data WHERE ppep = phosphopeptide GROUP BY kinase, ppep - ORDER BY kinase, ppep, p_value_data.quality DESC + ORDER BY kinase, p_value_data.quality DESC "), justification = "l l l l l l l", centered = TRUE,