Mercurial > repos > eschen42 > w4mcorcov
diff w4mcorcov_calc.R @ 2:e03582f26617 draft
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
author | eschen42 |
---|---|
date | Sun, 12 Nov 2017 19:45:36 -0500 |
parents | 0c2ad44b6c9c |
children | 5aaab36bc523 |
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--- a/w4mcorcov_calc.R Sun Oct 22 18:47:57 2017 -0400 +++ b/w4mcorcov_calc.R Sun Nov 12 19:45:36 2017 -0500 @@ -7,8 +7,8 @@ #### OPLS-DA algoC <- "nipals" -do_detail_plot <- function(x_dataMatrix, x_predictor, x_is_match, x_algorithm, x_prefix, x_show_labels, x_progress = print, x_env) { - off <- function(x) if (x_show_labels == "0") x else 0 +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) { + 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( x = x_dataMatrix @@ -34,7 +34,7 @@ lim_x <- max(sapply(X=c(min_x, max_x), FUN=abs)) covariance <- covariance / lim_x lim_x <- 1.2 - main_label <- sprintf("%s for levels %s versus %s", x_prefix, fctr_lvl_1, fctr_lvl_2) + main_label <- sprintf("%s for level %s versus %s", x_prefix, fctr_lvl_1, fctr_lvl_2) main_cex <- min(1.0, 46.0/nchar(main_label)) # "It is generally accepted that a variable should be selected if vj>1, [27–29], # but a proper threshold between 0.83 and 1.21 can yield more relevant variables according to [28]." @@ -50,8 +50,8 @@ y = plus_cor , x = plus_cov , type="p" - , xlim=c(-lim_x, lim_x + off(0.1)) - , ylim=c(-1.0 - off(0.1), 1.0) + , xlim=c( -lim_x - off(0.2), lim_x + off(0.2) ) + , ylim=c( -1.0 - off(0.2), 1.0 + off(0.2) ) , xlab = sprintf("relative covariance(feature,t1)") , ylab = sprintf("correlation(feature,t1)") , main = main_label @@ -62,8 +62,8 @@ ) low_x <- -0.7 * lim_x high_x <- 0.7 * lim_x - text(x = low_x, y = -0.05, labels = fctr_lvl_1) - text(x = high_x, y = 0.05, labels = fctr_lvl_2) + text(x = low_x, y = -0.05, labels = fctr_lvl_1, col = "blue") + text(x = high_x, y = 0.05, labels = fctr_lvl_2, col = "red") if ( x_show_labels != "0" ) { my_loadp <- loadp my_loado <- loado @@ -77,17 +77,22 @@ n_labels <- min( n_labels, (1 + length(loadp)) / 2 ) labels_to_show <- c( names(head(sort(my_loadp),n = n_labels)) - , names(head(sort(my_loado),n = n_labels)) , names(tail(sort(my_loadp),n = n_labels)) - , names(tail(sort(my_loado),n = n_labels)) ) + if ( x_show_loado_labels ) { + labels_to_show <- c( + labels_to_show + , names(head(sort(my_loado),n = n_labels)) + , names(tail(sort(my_loado),n = n_labels)) + ) + } labels <- unname(sapply( X = tsv1$featureID, FUN = function(x) if( x %in% labels_to_show ) x else "" )) text( y = plus_cor - 0.013 , x = plus_cov + 0.020 - , cex = 0.3 + , cex = 0.4 , labels = labels - , col = rgb(blue = blue, red = red, green = 0, alpha = 0.2 + 0.8 * alpha) + , col = rgb(blue = 0, red = 0, green = 0, alpha = 0.5) # rgb(blue = blue, red = red, green = 0, alpha = 0.2 + 0.8 * alpha) , srt = -30 # slant 30 degrees downward , adj = 0 # left-justified ) @@ -164,6 +169,7 @@ # matchingC is one of { "none", "wildcard", "regex" } matchingC <- calc_env$matchingC labelFeatures <- calc_env$labelFeatures + labelOrthoFeatures <- calc_env$labelOrthoFeatures # arg/env checking if (!(facC %in% names(smpl_metadata))) { @@ -297,6 +303,7 @@ , x_algorithm = algoC , x_prefix = if (pairSigFeatOnly) "Significantly contrasting features" else "Significant features" , x_show_labels = labelFeatures + , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action , x_env = calc_env ) @@ -352,6 +359,7 @@ , x_algorithm = algoC , x_prefix = if (pairSigFeatOnly) "Significantly contrasting features" else "Significant features" , x_show_labels = labelFeatures + , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action , x_env = calc_env ) @@ -404,6 +412,7 @@ , x_algorithm = algoC , x_prefix = "Features" , x_show_labels = labelFeatures + , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action , x_env = calc_env ) @@ -448,6 +457,7 @@ , x_algorithm = algoC , x_prefix = "Features" , x_show_labels = labelFeatures + , x_show_loado_labels = labelOrthoFeatures , x_progress = progress_action , x_env = calc_env )