Mercurial > repos > eschen42 > w4mcorcov
comparison w4mcorcov_calc.R @ 14:90708fdbc22d draft default tip
"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
| author | eschen42 |
|---|---|
| date | Wed, 18 Nov 2020 18:53:37 +0000 |
| parents | 2ae2d26e3270 |
| children |
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| 13:2ae2d26e3270 | 14:90708fdbc22d |
|---|---|
| 20 x = x_dataMatrix | 20 x = x_dataMatrix |
| 21 , y = x_predictor | 21 , y = x_predictor |
| 22 , algoC = x_algorithm | 22 , algoC = x_algorithm |
| 23 , predI = 1 | 23 , predI = 1 |
| 24 , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0 | 24 , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0 |
| 25 , printL = FALSE | 25 , fig.pdfC = 'none' |
| 26 , plotL = FALSE | 26 , info.txtC = 'none' |
| 27 , crossvalI = x_crossval_i | 27 , crossvalI = x_crossval_i |
| 28 , scaleC = "pareto" # data centered and pareto scaled here only. This line fixes issue #2. | 28 , scaleC = "pareto" # data centered and pareto scaled here only. This line fixes issue #2. |
| 29 ) | 29 ) |
| 30 # strip out variables having negligible variance | 30 # strip out variables having negligible variance |
| 31 x_dataMatrix <- x_dataMatrix[ , names(my_oplsda@vipVn), drop = FALSE] | 31 x_dataMatrix <- x_dataMatrix[ , names(my_oplsda@vipVn), drop = FALSE] |
| 441 # extract the levels from the environment | 441 # extract the levels from the environment |
| 442 originalLevCSV <- levCSV <- calc_env$levCSV | 442 originalLevCSV <- levCSV <- calc_env$levCSV |
| 443 # matchingC is one of { "none", "wildcard", "regex" } | 443 # matchingC is one of { "none", "wildcard", "regex" } |
| 444 matchingC <- calc_env$matchingC | 444 matchingC <- calc_env$matchingC |
| 445 labelFeatures <- calc_env$labelFeatures | 445 labelFeatures <- calc_env$labelFeatures |
| 446 minCrossvalI <- as.integer(calc_env$min_crossval_i) | |
| 446 | 447 |
| 447 # arg/env checking | 448 # arg/env checking |
| 448 if (!(facC %in% names(smpl_metadata))) { | 449 if (!(facC %in% names(smpl_metadata))) { |
| 449 failure_action( | 450 failure_action( |
| 450 sprintf("bad parameter! Factor name '%s' not found in sampleMetadata" | 451 sprintf("bad parameter! Factor name '%s' not found in sampleMetadata" |
| 598 } else { | 599 } else { |
| 599 "Significant features" | 600 "Significant features" |
| 600 } | 601 } |
| 601 , x_show_labels = labelFeatures | 602 , x_show_labels = labelFeatures |
| 602 , x_progress = progress_action | 603 , x_progress = progress_action |
| 603 , x_crossval_i = min(7, length(chosen_samples)) | 604 , x_crossval_i = min(minCrossvalI, length(chosen_samples)) |
| 604 , x_env = calc_env | 605 , x_env = calc_env |
| 605 ) | 606 ) |
| 606 if ( is.null(my_cor_cov) ) { | 607 if ( is.null(my_cor_cov) ) { |
| 607 progress_action("NOTHING TO PLOT") | 608 progress_action("NOTHING TO PLOT") |
| 608 } else { | 609 } else { |
| 672 } else { | 673 } else { |
| 673 "Significant features" | 674 "Significant features" |
| 674 } | 675 } |
| 675 , x_show_labels = labelFeatures | 676 , x_show_labels = labelFeatures |
| 676 , x_progress = progress_action | 677 , x_progress = progress_action |
| 677 , x_crossval_i = min(7, length(chosen_samples)) | 678 , x_crossval_i = min(minCrossvalI, length(chosen_samples)) |
| 678 , x_env = calc_env | 679 , x_env = calc_env |
| 679 ) | 680 ) |
| 680 if ( is.null(my_cor_cov) ) { | 681 if ( is.null(my_cor_cov) ) { |
| 681 progress_action("NOTHING TO PLOT.") | 682 progress_action("NOTHING TO PLOT.") |
| 682 } else { | 683 } else { |
| 751 , x_is_match = is_match | 752 , x_is_match = is_match |
| 752 , x_algorithm = "nipals" | 753 , x_algorithm = "nipals" |
| 753 , x_prefix = "Features" | 754 , x_prefix = "Features" |
| 754 , x_show_labels = labelFeatures | 755 , x_show_labels = labelFeatures |
| 755 , x_progress = progress_action | 756 , x_progress = progress_action |
| 756 , x_crossval_i = min(7, length(chosen_samples)) | 757 , x_crossval_i = min(minCrossvalI, length(chosen_samples)) |
| 757 , x_env = calc_env | 758 , x_env = calc_env |
| 758 ) | 759 ) |
| 759 if ( is.null(my_cor_cov) ) { | 760 if ( is.null(my_cor_cov) ) { |
| 760 progress_action("NOTHING TO PLOT...") | 761 progress_action("NOTHING TO PLOT...") |
| 761 } else { | 762 } else { |
| 804 , x_is_match = is_match | 805 , x_is_match = is_match |
| 805 , x_algorithm = "nipals" | 806 , x_algorithm = "nipals" |
| 806 , x_prefix = "Features" | 807 , x_prefix = "Features" |
| 807 , x_show_labels = labelFeatures | 808 , x_show_labels = labelFeatures |
| 808 , x_progress = progress_action | 809 , x_progress = progress_action |
| 809 , x_crossval_i = min(7, length(chosen_samples)) | 810 , x_crossval_i = min(minCrossvalI, length(chosen_samples)) |
| 810 , x_env = calc_env | 811 , x_env = calc_env |
| 811 ) | 812 ) |
| 812 if ( is.null(my_cor_cov) ) { | 813 if ( is.null(my_cor_cov) ) { |
| 813 progress_action("NOTHING TO PLOT.....") | 814 progress_action("NOTHING TO PLOT.....") |
| 814 } else { | 815 } else { |