volcanoPlot {circRNAprofiler} | R Documentation |
The function volcanoPlot() generates a volcano plot with the results of the differential expression analysis.
volcanoPlot( res, log2FC = 1, padj = 0.05, title = "", gene = FALSE, geneSet = c(""), setxLim = FALSE, xlim = c(-8, 8), setyLim = FALSE, ylim = c(0, 5), color = "blue" )
res |
A data frame containing the the differential expression resuls.
It can be generated with |
log2FC |
An integer specifying the log2FC cut-off. Deafult value is 1. |
padj |
An integer specifying the adjusted P value cut-off. Deafult value is 0.05. |
title |
A character string specifying the title of the plot. |
gene |
A logical specifying whether to show all the host gene names of the differentially expressed circRNAs to the plot. Deafult value is FALSE. |
geneSet |
A character vector specifying which host gene name of the differentially expressed circRNAs to show in the plot. Multiple host gene names can be specofied. E.g. c('TTN, RyR2') |
setxLim |
A logical specifying whether to set x scale limits. If TRUE the value in xlim will be used. Deafult value is FALSE. |
xlim |
A numeric vector specifying the lower and upper x axis limits. Deafult values are c(-8 , 8). |
setyLim |
A logical specifying whether to set y scale limits. If TRUE the value in ylim will be used. Deafult value is FALSE. |
ylim |
An integer specifying the lower and upper y axis limits Deafult values are c(0, 5). |
color |
A string specifying the color of the differentially expressed circRNAs. Default value is "blue". |
A ggplot object.
# Load data frame containing detected back-spliced junctions data("mergedBSJunctions") pathToExperiment <- system.file("extdata", "experiment.txt", package ="circRNAprofiler") # Filter circRNAs filterdCirc <- filterCirc( mergedBSJunctions, allSamples = FALSE, min = 5, pathToExperiment) # Find differentially expressed circRNAs deseqResBvsA <- getDeseqRes( filterdCirc, condition = "A-B", pAdjustMethod = "BH", pathToExperiment) # Plot p <- volcanoPlot( deseqResBvsA, log2FC = 1, padj = 0.05, title = "", setxLim = TRUE, xlim = c(-8 , 7.5), setyLim = FALSE, ylim = c(0 , 4), gene = FALSE) p