R/ebbc_plot_thresholds.R

In LeonardoRicci/EBBC: Expression-Based Bayesian Classifier

## --------------------------------------------------------------------------
##
## This file is part of the EBBC software package.
##
## Version 1.0 - January 2020
##
##
## The EBBC package is free software; you can use it, redistribute it,
## and/or modify it under the terms of the GNU General Public License
## version 3 as published by the Free Software Foundation. The full text
## of the license can be found in the file LICENSE.txt at the top level of
## the package distribution.
##
## Authors:
##	Michele Castelluzzo (1), Alessio Perinelli (1),
##		Michela A. Denti (2) and Leonardo Ricci (1,3)
##	(1) Department of Physics, University of Trento, 38123 Trento, Italy
##	(2) Department of Cellular, Computational and Integrative Biology
##		(CIBIO), University of Trento, 38123 Trento, Italy
##	(3) CIMeC, Center for Mind/Brain Sciences, University of Trento,
##		38068 Rovereto, Italy
##
##	michele.castelluzzo@unitn.it
##	alessio.perinelli@unitn.it
##	michela.denti@unitn.it
##	leonardo.ricci@unitn.it
##	https://github.com/LeonardoRicci/
##	https://nse.physics.unitn.it/
##
##
## If you use the EBBC package for your analyses, please cite:
##
##	L. Ricci, V. Del Vescovo, C. Cantaloni, M. Grasso, M. Barbareschi and
##	M. A. Denti, Statistical analysis of a Bayesian classifier based on the
##	expression of miRNAs, BMC Bioinformatics 16:287 (2015).
##	DOI: 10.1186/s12859-015-0715-9
##
##
## --------------------------------------------------------------------------

#' Plot of scores and thresholds of a Bayes classifier.
#'
#' Generates a plot of the classifier scores of a dataset, as well as the corresponding classifier thresholds.
#'
#' @param inputDataset Dataset (data frame) to be used for the plot.
#' @param thresholdsFrame Threshold values (data frame) to be used for the plot.
#' @param outputFileLabel Label to be used to build the name of the output file.
#' @param plotFormat String to set the format of the output file. Can either be 'pdf' (default) or 'png'.
#'
#' @return A ggplot object containing the plot.
#'
#' This function is not exported to the ebbc package NAMESPACE, but it is called by other functions of the same package.

ebbc_plotThresholds <- function(inputDataset, thresholdsFrame, outputFileLabel, plotFormat="pdf") {

	title <- "Classification results"
	size <- 24

	dnorm.count <- function(x, mean = 0, sd = 1, log = FALSE, n = 1, binwidth = 1) {
		n * binwidth * stats::dnorm(x = x, mean = mean, sd = sd, log = log)
	}

	dataTarget <- subset(inputDataset, inputDataset$Classification == 'target')
	dataVersus <- subset(inputDataset, inputDataset$Classification == 'versus')

	maxPlot <- round(max(inputDataset$Score)+0.5,0)
	minPlot <- round(min(inputDataset$Score)-0.5,0)

	chi <- as.numeric(as.vector(thresholdsFrame$Threshold))
	dchi <- as.numeric(as.vector(thresholdsFrame$DeltaThreshold))
	chiUp <- as.numeric(as.vector(thresholdsFrame$ChiUp))
	dchiUp <- as.numeric(as.vector(thresholdsFrame$DChiUp))
	chiDown <- as.numeric(as.vector(thresholdsFrame$ChiDown))
	dchiDown <- as.numeric(as.vector(thresholdsFrame$DChiDown))

	rects <- data.frame(ystart = c(-Inf,chiDown,chi,chiUp), yend = c(chiDown,chi,chiUp,Inf), Classification = c("4", "3", "2", "1"))
	plotObject <- ggplot2::ggplot() +
		ggplot2::theme(legend.title=ggplot2::element_text(size=14)) +
		ggplot2::theme(legend.text=ggplot2::element_text(size=14)) +
		ggplot2::geom_rect(data = rects, ggplot2::aes(xmin=-Inf, xmax=Inf, ymin=rects$ystart, ymax=rects$yend, fill=rects$Classification), alpha = 0.4) +
		ggplot2::scale_fill_manual(name= "Score", values= c("green", "lightgreen", "yellow", "orange"), labels=c("target", "", "", "versus")) +
		ggplot2::ggtitle(title) +
		ggplot2::theme(plot.title = ggplot2::element_text(lineheight=.8, size=size, face="bold", hjust = 0.25, vjust = -5)) +
		ggplot2::xlab("sample #") + ggplot2::ylab("y") +
		ggplot2::theme(axis.text=ggplot2::element_text(size=14,face="bold",color=1), axis.title=ggplot2::element_text(size=20,face="bold")) +
		ggplot2::scale_x_continuous(breaks=seq(0,dim(inputDataset)[1],length.out=5)) +
		ggplot2::scale_y_continuous(breaks=seq(minPlot,maxPlot,length.out=11), limits=c(minPlot, maxPlot)) +
		ggplot2::geom_point(data=inputDataset, ggplot2::aes(x=1:nrow(inputDataset), y=inputDataset$Score, color=inputDataset$Classification), size=3) +
		ggplot2::scale_colour_manual(name="Classification", values=c("blue", "red")) +
		ggplot2::geom_hline(yintercept=max(chi), linetype=1, color="black", size = 1.2) +
		ggplot2::geom_hline(yintercept=max(chi+dchi), linetype=4, color="black", size = 0.6) +
		ggplot2::geom_hline(yintercept=max(chi-dchi), linetype=4, color="black", size = 0.6) +
		ggplot2::geom_hline(yintercept=max(chiUp), linetype=1, color="blue", size = 1.0) +
		ggplot2::geom_hline(yintercept=max(chiUp+dchiUp), linetype=4, color="blue", size = 0.6) +
		ggplot2::geom_hline(yintercept=max(chiUp-dchiUp), linetype=4, color="blue", size = 0.6) +
		ggplot2::geom_hline(yintercept=max(chiDown), linetype=1, color="red", size = 1.0) +
		ggplot2::geom_hline(yintercept=max(chiDown+dchiDown), linetype=4, color="red", size = 0.6) +
		ggplot2::geom_hline(yintercept=max(chiDown-dchiDown), linetype=4, color="red", size = 0.6) +

	switch(plotFormat,
		png = suppressMessages(ggplot2::ggsave(paste(sep="", outputFileLabel, "_scores.png"), device="png")),		# png case
		suppressMessages(ggplot2::ggsave(paste(sep="", outputFileLabel, "_scores.pdf"), device=grDevices::cairo_pdf))	# default pdf
	)

	return(plotObject)
}