Mercurial > repos > eschen42 > w4mcorcov

comparison w4mcorcov_calc.R @ 14:90708fdbc22d draft default tip

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"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
comparison
equal deleted inserted replaced
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 {