Nothing
#' VSEplot
#'
#' This function will generate a figure for VSE analysis
#' @param data A list of matrices outputted by the function VariantSetEnrichment
#' @param padj Bonferroni adjusted p-value cutoff. Default: 0.01
#' @param ... Arguments from boxplot
#' @keywords VSE, boxplot
#' @examples
#' #Load pre-saved object "bca.vse" as an example VSE output
#' load(file.path(system.file("extdata", "vse_output.Rda", package="VSE")))
#' VSEplot(bca.vse, las=2,pch=20, cex=1, cex.main=0.6, padj=0.05)
#' @export
VSEplot <- function(data, padj=0.01, ...){
matrix_norm <- data[[2]]
matrix_scaled <- data[[3]]
p_values <- c()
for (i in 1:nrow(matrix_scaled)){
avs <- matrix_scaled[i,1]
null <- matrix_scaled[i,c(2:ncol(matrix_scaled))]
p <- 1 - pnorm(matrix_scaled[i,], mean(matrix_scaled[i,]), sd(matrix_scaled[i,]))
p_values[i] <- p[1]
}
padjust_values <- p.adjust(p_values, method = "bonferroni")
boxplot(t(matrix_scaled), ylim=c( min(matrix_scaled),max(matrix_scaled) ), ylab="Enrichment Score", outline=FALSE, notch=TRUE, ...)
for (i in 1:length(padjust_values)){
points(i,matrix_scaled[i,1], pch=19, col=ifelse(padjust_values[i] <= padj, "red","black"))
}
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.