DrawDistriHistBox: DrawDistriHistBox Function (GloModAn)

In AlexisHardy/DNAModAnnot: Toolbox for DNA Modifications filtering and annotation

DrawDistriHistBox Function (GloModAn)

Description

Return a line-plot describing the cumulative length of contigs (ordered from largest to smallest contig).

Usage

DrawDistriHistBox(
  nParam,
  cGraphName,
  cParamName,
  lTrimOutliers = FALSE,
  nXLimits = NULL
)

Arguments

nParam	A numeric vector containing the parameter values to be plotted.
cGraphName	The graph name to be displayed on top of the plot.
cParamName	The name of the parameter to be displayed below the x-axis.
lTrimOutliers	If TRUE, remove the outliers from the boxplot and trim the histogram to the borders of the boxplot. Defaults to FALSE.
nXLimits	A numeric vector giving the limits of the plot on the x-axis. If NULL, the limits will be set to the minimum and the maximum of the nParam data (or to the inner fences (1.5*Interquartile Range) of the boxplot if lTrimmingOutliers is TRUE). Defaults to NULL.

Examples

# loading genome
myGenome <- Biostrings::readDNAStringSet(system.file(
  package = "DNAModAnnot", "extdata",
  "ptetraurelia_mac_51_sca171819.fa"
))

# Preparing a gposPacBioCSV dataset
myGposPacBioCSV <-
  ImportPacBioCSV(
    cPacBioCSVPath = system.file(
      package = "DNAModAnnot", "extdata",
      "ptetraurelia.bases.sca171819.csv"
    ),
    cSelectColumnsToExtract = c(
      "refName", "tpl", "strand", "base",
      "score", "ipdRatio", "coverage"
    ),
    lKeepExtraColumnsInGPos = TRUE, lSortGPos = TRUE,
    cContigToBeAnalyzed = names(myGenome)
  )

DrawDistriHistBox(head(myGposPacBioCSV$coverage, 100000),
  cGraphName = "Coverage distribution of some bases sequenced",
  cParamName = "Coverage",
  lTrimOutliers = TRUE
)

AlexisHardy/DNAModAnnot documentation built on Feb. 27, 2023, 12:03 a.m.