BadRegionFinder (version 1.0.0)

plotSummary: Plots a summary of the coverage quality

Description

The function plotSummary provides a possibility to visualize the output of reportBadRegionsSummary. A line graph is returned, visualizing the number of bases that fall into each category of coverage quality. Furthermore, information on the genes located in these regions is included.

Usage

plotSummary(threshold1, threshold2, percentage1, percentage2,  badCoverageSummary, output)

Arguments

threshold1

Integer, threshold defining the number of reads that have to be registered for a sample that its coverage is classified as acceptable.

threshold2

Integer, threshold defining the number of reads that have to be registered for a sample that its coverage is classified as good.

percentage1

Float, defining the percentage of samples that have to feature a coverage of at least threshold1 so that the position is classified as acceptably covered.

percentage2

Float, defining the percentage of samples that have to feature a coverage of at least threshold2 so that the position is classified as well covered.

badCoverageSummary

GRanges object, return value of function reportBadRegionsSummary.

output

The folder to write the output file into. If this argument is an empty string, the plot is printed on the screen.

Value

No value is returned.

Details

The function plotSummary serves to summarize the previously determined coverage quality in a visual way.

On the y axis the coverage quality is coded. The different categories are color coded as well as height coded. As numbers from 0 to 5 were previously assigned to the different categories, thick lines are now drawn at the height of the category. Furthermore, the categories are color coded in the following way: red - bad region on target; yellow - acceptable region on target; green - good region on target; black - bad region off target; dark gray - acceptable region off target; light gray - good region off target.

On the x axis the detected genes are printed. Wherever a new region covering a new gene is registered, a dashed line is drawn.

See Also

BadRegionFinder, determineCoverage, determineCoverageQuality, determineRegionsOfInterest, reportBadRegionsSummary, reportBadRegionsDetailed, reportBadRegionsGenes, plotDetailed, plotSummaryGenes, determineQuantiles

Examples

library("BSgenome.Hsapiens.UCSC.hg19")

threshold1 <- 20
threshold2 <- 100
percentage1 <- 0.80
percentage2 <- 0.90
sample_file <- system.file("extdata", "SampleNames.txt", 
                           package = "BadRegionFinder")
samples <- read.table(sample_file)
bam_input <- system.file("extdata", package = "BadRegionFinder")
output <- system.file("extdata", package = "BadRegionFinder")
target_regions <- system.file("extdata", "targetRegions.bed",
                              package = "BadRegionFinder")
targetRegions <- read.table(target_regions, header = FALSE,
                            stringsAsFactors = FALSE)

coverage_summary <- determineCoverage(samples, bam_input, targetRegions, output,
                                      TRonly = TRUE)
coverage_indicators <- determineCoverageQuality(threshold1, threshold2,
                                                percentage1, percentage2,
                                                coverage_summary)
badCoverageSummary <- reportBadRegionsSummary(threshold1, threshold2,
                                              percentage1, percentage2,
                                              coverage_indicators, "", output)
plotSummary(threshold1, threshold2, percentage1, percentage2, 
            badCoverageSummary, output)