Mercurial > repos > eschen42 > w4mcorcov
comparison w4mcorcov_wrapper.R @ 13:2ae2d26e3270 draft
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
| author | eschen42 |
|---|---|
| date | Wed, 12 Dec 2018 09:20:02 -0500 |
| parents | ddcc33ff3205 |
| children | 90708fdbc22d |
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| 12:ddaf84e15d06 | 13:2ae2d26e3270 |
|---|---|
| 71 ######## | 71 ######## |
| 72 # MAIN # | 72 # MAIN # |
| 73 ######## | 73 ######## |
| 74 | 74 |
| 75 errorPrint(sessionInfo()) | 75 errorPrint(sessionInfo()) |
| 76 errorCat("\nsearch path:") | |
| 77 errorPrint(search()) | |
| 78 # errorCat("\nCurrently loaded namespaces:\n") | |
| 79 # errorPrint(loadedNamespaces()) | |
| 76 | 80 |
| 77 argVc <- unlist(parseCommandArgs(evaluate=FALSE)) | 81 argVc <- unlist(parseCommandArgs(evaluate=FALSE)) |
| 78 errorCat("\n\n---\n\nArguments that were passed to R are as follows:\n") | 82 errorCat("\n\n---\n\nArguments that were passed to R are as follows:\n") |
| 79 errorPrint(argVc) | 83 errorPrint(argVc) |
| 80 | 84 |
| 102 my_env$facC <- as.character(argVc["facC"]) | 106 my_env$facC <- as.character(argVc["facC"]) |
| 103 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) | 107 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) |
| 104 my_env$levCSV <- as.character(argVc["levCSV"]) | 108 my_env$levCSV <- as.character(argVc["levCSV"]) |
| 105 my_env$matchingC <- as.character(argVc["matchingC"]) | 109 my_env$matchingC <- as.character(argVc["matchingC"]) |
| 106 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' | 110 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' |
| 111 my_env$fdr_features <- as.character(argVc["fdr_features"]) # number of features to consider when adjusting p-value, or 'ALL' | |
| 107 my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested | 112 my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested |
| 108 my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested | 113 my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested |
| 109 my_env$cplot_y <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot | 114 my_env$cplot_y <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot |
| 110 | 115 |
| 111 label_features <- my_env$labelFeatures | 116 label_features <- my_env$labelFeatures |