R/plots.R

In permubiome: A Permutation Based Test for Biomarker Discovery in Microbiome Data

plots <-
function ()
{
Class<-NULL
non_zero<-NULL
Occurring<-NULL
prevalence<-NULL
ref<-NULL
loadNamespace("ggplot2")
loadNamespace("Matrix")
load("permubiome.RData")
df_norm <- df_norm
category <- readline("Type the category you want to plot : ")
if (category == ""){
category <- colnames(df_norm[3])
print(paste("As you declared no categories, the very first one of your dataset is plotted!"))
}
df_to_plot <- df_norm[,c("Sample","Class",category)]
classes<-levels(df_to_plot$Class)
if (REFERENCE == ""){
REFERENCE <- classes[1]
} else if (REFERENCE == classes[2]){
classes[2] <- classes[1]
classes[1] <- REFERENCE
}
df_to_plot$ref <- factor(df_to_plot$Class, levels=(c(classes[1],classes[2])))
p1<-(ggplot(df_to_plot, aes(ref, df_to_plot[,category], fill=Class), environment = environment()))+
	geom_boxplot(notch=F, outlier.colour="blue", outlier.shape=1, outlier.size=3)+
	geom_point(colour="#000000", size=2.5, pch=19)+
	scale_fill_manual(values=c("#E41A1C", "#377EB8"))+
	ggtitle(category)+
	guides(fill=FALSE)+
	theme(plot.title=element_text(size=24, face="bold"))+
	ylab("Normalized read proportion")+
	xlab("Classes")+
	theme(axis.text=element_text(size=12), axis.title=element_text(size=16,face="bold"))+
	coord_flip()+
	theme(plot.margin = unit(c(0.25,0.25,0.25,0.25), "cm"))
	
non_zero<-as.data.frame((tapply(df_to_plot[[category]], df_to_plot$ref, nnzero)))
total<-as.data.frame((tapply(df_to_plot[[category]], df_to_plot$ref, length)))
prevalence_table<-data.frame(names = factor(c(classes[1], classes[2]), levels=c(classes[1], classes[2])), Occurring=c(non_zero[,1]), Subjects=c(total[,1]))
prevalence_table$prevalence<-(prevalence_table$Occurring/prevalence_table$Subjects)*100

p2<-ggplot(prevalence_table, aes(x=names, y=prevalence, fill=names, width=0.75))+
	geom_bar(stat="identity", colour="grey20")+
	scale_fill_manual(values=c("#E41A1C", "#377EB8"))+
	coord_flip()+
	guides(fill=FALSE)+
	ggtitle(paste("", "", sep=" "))+
	theme(plot.title=element_text(size=24, face="bold"))+
	ylab("Prevalence (%)")+
	theme(axis.title.y=element_blank(), axis.text.y=element_blank(),axis.text.x=element_text(size=12),axis.title=element_text(size=16,face="bold"))+
	theme(plot.margin = unit(c(0.25,0.25,0.25,0.25), "cm"))+
	ylim(0,100)
output <- readline("Do you want an output file (yes/no)? : ")
if (substr(output, 1, 1) == "y"){
extension <- readline("What extension do you prefer for the output plot (ps, pdf, jpeg, tiff, png, bmp )? : ")
tiff(filename=paste(category, extension, sep = "."), width=1000, height=200, res=100, units="px")
grid.arrange(p1, p2, ncol=2)
dev.off()
} 
else
{
print(grid.arrange(p1, p2, ncol=2))
}
save(df, df_norm, df_to_plot, REFERENCE, classes, file="permubiome.RData")
}