| Previous changeset 2:e03582f26617 (2017-11-12) Next changeset 4:8bba31f628da (2018-03-04) |
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Commit message:
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 88004a3cf8868d68da1ec5bd2c1be53746350367 |
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modified:
w4mcorcov.xml w4mcorcov_calc.R |
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| diff -r e03582f26617 -r 5aaab36bc523 w4mcorcov.xml --- a/w4mcorcov.xml Sun Nov 12 19:45:36 2017 -0500 +++ b/w4mcorcov.xml Mon Jan 15 14:30:15 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.5"> +<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.6"> <description>OPLS-DA Contrasts of Univariate Results</description> @@ -651,6 +651,10 @@ Release notes ------------- +0.98.6 + +- bug fix: set 'crossvalI' param (of R function 'ropls::opls') to the number of samples when the there are fewer than seven samples. + 0.98.5 - bug fix: fit feature-labels within clipping region of cor-vs.cov plot |
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| diff -r e03582f26617 -r 5aaab36bc523 w4mcorcov_calc.R --- a/w4mcorcov_calc.R Sun Nov 12 19:45:36 2017 -0500 +++ b/w4mcorcov_calc.R Mon Jan 15 14:30:15 2018 -0500 |
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| @@ -7,7 +7,7 @@ #### OPLS-DA algoC <- "nipals" -do_detail_plot <- function(x_dataMatrix, x_predictor, x_is_match, x_algorithm, x_prefix, x_show_labels, x_show_loado_labels, x_progress = print, x_env) { +do_detail_plot <- function(x_dataMatrix, x_predictor, x_is_match, x_algorithm, x_prefix, x_show_labels, x_show_loado_labels, x_progress = print, x_env, x_crossval_i) { off <- function(x) if (x_show_labels == "0") 0 else x if (x_is_match && ncol(x_dataMatrix) > 0 && length(unique(x_predictor))> 1) { my_oplsda <- opls( @@ -18,6 +18,7 @@ , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0 , printL = FALSE , plotL = FALSE + , crossvalI = x_crossval_i ) my_oplsda_suppLs_y_levels <- levels(as.factor(my_oplsda@suppLs$y)) fctr_lvl_1 <- my_oplsda_suppLs_y_levels[1] @@ -305,6 +306,7 @@ , x_show_labels = labelFeatures , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action + , x_crossval_i = min(7, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { @@ -361,6 +363,7 @@ , x_show_labels = labelFeatures , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action + , x_crossval_i = min(7, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { @@ -414,6 +417,7 @@ , x_show_labels = labelFeatures , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action + , x_crossval_i = min(7, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { @@ -459,6 +463,7 @@ , x_show_labels = labelFeatures , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action + , x_crossval_i = min(7, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { |