small changes to help text for v. 0.6.0

svkucheryavski · Jan 15, 2015 · c8b18d4 · c8b18d4
1 parent 908b094
commit c8b18d4
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Showing 6 changed files with 31 additions and 15 deletions.
diff --git a/R/randtest.R b/R/randtest.R
@@ -97,11 +97,13 @@ randtest = function(x, y, ncomp = 15, center = T, scale = F, nperm = 1000,
 #' label for x axis
 #' @param ylab
 #' label for y axis
+#' @param ...
+#' other optional arguments
 #' 
 #' @details
 #' See examples in help for \code{\link{randtest}} function.
 #' 
-plotHist.randtest = function(obj, comp = NULL, main = NULL, xlab = 'Test statistic', ylab = 'Frequency')    
+plotHist.randtest = function(obj, comp = NULL, main = NULL, xlab = 'Test statistic', ylab = 'Frequency', ...)    
 {
    if (is.null(comp))
       comp = obj$ncomp.selected
@@ -139,11 +141,13 @@ plotHist.randtest = function(obj, comp = NULL, main = NULL, xlab = 'Test statist
 #' label for x axis
 #' @param ylab
 #' label for y axis
+#' @param ...
+#' other optional arguments
 #' 
 #' @details
 #' See examples in help for \code{\link{randtest}} function.
 #' 
-plotCorr.randtest = function(obj, comp = NULL, main = NULL, xlab = expression(r^2), ylab = 'Test statistic')
+plotCorr.randtest = function(obj, comp = NULL, main = NULL, xlab = expression(r^2), ylab = 'Test statistic', ...)
 {
    if (is.null(comp))
       comp = obj$ncomp.selected
@@ -154,31 +158,37 @@ plotCorr.randtest = function(obj, comp = NULL, main = NULL, xlab = expression(r^
    data = list(cbind(obj$corrperm[, comp]^2, obj$statperm[, comp]), cbind(1, obj$stat[, comp]))   
    fitdata = rbind(apply(data[[1]], 2, mean), data[[2]])
 
-   mdaplotg(data, type = 'p', main = main, xlab = xlab, ylab = ylab)
+   mdaplotg(data, type = 'p', main = main, xlab = xlab, ylab = ylab, ...)
    mdaplot.showRegressionLine(fitdata, col = rgb(0.6, 0.6, 0.6), lty = 2, lwd = 0.75)
 }
 
 #' Plot for randomization test results
 #' 
+#' @method plot randtest
+#' @S3method plot randtest
+#' 
 #' @description
 #' Makes a bar plot with alpha values for each component.
 #' 
-#' @param obj
+#' @param x
 #' results of randomization test (object of class `randtest`)
 #' @param main
 #' main title for the plot
 #' @param xlab
 #' label for x axis
 #' @param ylab
 #' label for y axis
+#' @param ...
+#' other optional arguments
 #' 
 #' @details
 #' See examples in help for \code{\link{randtest}} function.
 #' 
-plot.randtest = function(obj, main = 'Alpha', xlab = 'Components', ylab = '')
+plot.randtest = function(x, main = 'Alpha', xlab = 'Components', ylab = '', ...)
 {
+   obj = x
    mdaplot(t(rbind(1:length(obj$alpha), obj$alpha)), show.lines = c(NA, 0.05), type = 'h', 
-           main = main, xlab = xlab, ylab = ylab)      
+           main = main, xlab = xlab, ylab = ylab, ...)      
 }
 
 #' Summary method for randtest object

diff --git a/man/mdaplotg.Rd b/man/mdaplotg.Rd
@@ -11,7 +11,7 @@ Plotting function for several sets of objects
 
 \usage{
 mdaplotg(data, type = 'p', pch = 16, lty = 1, lwd = 1, bwd = 0.8, legend = NULL, 
-   xlab = NA, ylab = NA, main = NULL, labels = NULL, 
+   xlab = NULL, ylab = NULL, main = NULL, labels = NULL, 
    ylim = NULL, xlim = NULL, colmap = 'default', 
    legend.position = "topright", single.x = T, 
    show.legend = T, show.labels = F, show.lines = F, show.grid = T, 

diff --git a/man/plot.randtest.Rd b/man/plot.randtest.Rd
@@ -4,17 +4,19 @@
 \alias{plot.randtest}
 \title{Plot for randomization test results}
 \usage{
-\method{plot}{randtest}(obj, main = "Alpha", xlab = "Components",
-  ylab = "")
+\method{plot}{randtest}(x, main = "Alpha", xlab = "Components", ylab = "",
+  ...)
 }
 \arguments{
-\item{obj}{results of randomization test (object of class `randtest`)}
+\item{x}{results of randomization test (object of class `randtest`)}
 
 \item{main}{main title for the plot}
 
 \item{xlab}{label for x axis}
 
 \item{ylab}{label for y axis}
+
+\item{...}{other optional arguments}
 }
 \description{
 Makes a bar plot with alpha values for each component.

diff --git a/man/plotCorr.randtest.Rd b/man/plotCorr.randtest.Rd
@@ -5,7 +5,7 @@
 \title{Correlation plot for randomization test results}
 \usage{
 \method{plotCorr}{randtest}(obj, comp = NULL, main = NULL,
-  xlab = expression(r^2), ylab = "Test statistic")
+  xlab = expression(r^2), ylab = "Test statistic", ...)
 }
 \arguments{
 \item{obj}{results of randomization test (object of class `randtest`)}
@@ -17,6 +17,8 @@
 \item{xlab}{label for x axis}
 
 \item{ylab}{label for y axis}
+
+\item{...}{other optional arguments}
 }
 \description{
 Makes a plot with statistic values vs. coefficient of determination between permuted

diff --git a/man/plotHist.randtest.Rd b/man/plotHist.randtest.Rd
@@ -5,7 +5,7 @@
 \title{Histogram plot for randomization test results}
 \usage{
 \method{plotHist}{randtest}(obj, comp = NULL, main = NULL,
-  xlab = "Test statistic", ylab = "Frequency")
+  xlab = "Test statistic", ylab = "Frequency", ...)
 }
 \arguments{
 \item{obj}{results of randomization test (object of class `randtest`)}
@@ -17,6 +17,8 @@
 \item{xlab}{label for x axis}
 
 \item{ylab}{label for y axis}
+
+\item{...}{other optional arguments}
 }
 \description{
 Makes a histogram for statistic values distribution for particular component, also

diff --git a/man/randtest.Rd b/man/randtest.Rd
@@ -3,8 +3,8 @@
 \title{Randomization test for PLS regression}
 
 \usage{
-   randtest = function(x, y, ncomp = 15, center = T, scale = F, nperm = 1000, 
-                    sig.level = 0.05, silent = TRUE)
+randtest(x, y, ncomp = 15, center = T, scale = F, nperm = 1000, 
+   sig.level = 0.05, silent = TRUE)
 }
 
 \description{
@@ -73,7 +73,7 @@ x = simdata$spectra.c
 x = prep.snv(x)
 
 ## Run the test and show summary
-r = randtest(x, y, ncomp = 5, nperm = 2000, silent = F)
+r = randtest(x, y, ncomp = 5, nperm = 2000, silent = FALSE)
 summary(r)
 
 ## Show plots