AddToModBasePropDistFromFeaturePlot: AddToModBasePropDistFromFeaturePlot Function (ModAnnot)

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

AddToModBasePropDistFromFeaturePlot Function (ModAnnot)

Description

Add an additional axis with data on a plot generated by DrawModBasePropDistFromFeature function.

Usage

AddToModBasePropDistFromFeaturePlot(
  dPosCountsDistFeatureStart,
  dPosCountsDistFeatureEnd = NULL,
  cSubtitleContent,
  cParamYLabel,
  cParamColor = "cyan3",
  cParamType = "l",
  cParamLwd = 3,
  cParamLty = 3,
  lAddAxisOnLeftSide = TRUE,
  nYLimits = NULL
)

Arguments

dPosCountsDistFeatureStart	A dataframe containing the data counts by distance to feature positions.
dPosCountsDistFeatureEnd	A second dataframe containing the data counts by distance to the second feature positions. If NULL, only 1 position will be plotted (featureStart). Defaults to NULL.
cSubtitleContent	A character vector giving the content of the subtitle to add below the title of the plot.
cParamYLabel	A character vector giving the content of the label on the new Y axis to add on the plot.
cParamColor	The color of the line and new axis to be added. Defaults to "cyan3".
cParamType	The type of plot to be added. See "type" argument plot base function. Defaults to "l".
cParamLwd	The width of the line/points to be added. Defaults to 3.
cParamLty	If a line is plotted, change the type of the line to be added. Defaults to 3.
lAddAxisOnLeftSide	If TRUE, add the new axis on the left side of the plot. If FALSE, add the new axis on the right side of the plot. Defaults to TRUE.
nYLimits	Numeric vector giving the limits for the new Y axis. Defaults to NULL (will use the minimum and the maximum of both data provided (dPosCountsDistFeatureStart and dPosCountsDistFeatureEnd)).

Examples

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

# loading annotation
myAnnotations <- rtracklayer::readGFFAsGRanges(system.file(
  package = "DNAModAnnot", "extdata",
  "ptetraurelia_mac_51_annotation_v2.0_sca171819.gff3"
))

# Preparing a grangesPacBioGFF and a grangesPacBioCSV datasets
myGrangesPacBioGFF <-
  ImportPacBioGFF(
    cPacBioGFFPath = system.file(
      package = "DNAModAnnot", "extdata",
      "ptetraurelia.modifications.sca171819.gff"
    ),
    cNameModToExtract = "m6A",
    cModNameInOutput = "6mA",
    cContigToBeAnalyzed = names(myGenome)
  )
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)
  )

# Retrieve, in a list, dataframes of ModBase counts per Distance values from feature positions
myModDistCountsList <- GetDistFromFeaturePos(
  grangesAnnotations = myAnnotations,
  cSelectFeature = "gene",
  grangesData = myGrangesPacBioGFF,
  lGetGRangesInsteadOfListCounts = FALSE,
  lGetPropInsteadOfCounts = TRUE,
  cWhichStrandVsFeaturePos = "both", nWindowSizeAroundFeaturePos = 600,
  lAddCorrectedDistFrom5pTo3p = TRUE,
  cFeaturePosNames = c("TSS", "TTS")
)
myBaseDistCountsList <- GetDistFromFeaturePos(
  grangesAnnotations = myAnnotations,
  cSelectFeature = "gene",
  grangesData = myGposPacBioCSV,
  lGetGRangesInsteadOfListCounts = FALSE,
  lGetPropInsteadOfCounts = TRUE,
  cWhichStrandVsFeaturePos = "both", nWindowSizeAroundFeaturePos = 600,
  lAddCorrectedDistFrom5pTo3p = TRUE,
  cFeaturePosNames = c("TSS", "TTS")
)
DrawModBasePropDistFromFeature(
  listModCountsDistDataframe = myModDistCountsList,
  listBaseCountsDistDataframe = myBaseDistCountsList,
  cFeaturePosNames = c("TSS", "TTS"),
  cBaseMotif = "A",
  cModMotif = "6mA"
)

# Loading Bam data
myBamfile <- Rsamtools::BamFile(file = system.file(
  package = "DNAModAnnot", "extdata",
  "PTET_MonoNuc_3-2new.pe.sca171819.sorted.bam"
))
myBam_GRanges <- as(GenomicAlignments::readGAlignments(myBamfile), "GRanges")
myBam_GRanges <- GetGposCenterFromGRanges(grangesData = myBam_GRanges)

# Retrieve dataframes of Read center counts per Distance values in a list
myCountsDist_List_bamfile <- GetDistFromFeaturePos(
  grangesAnnotations = myAnnotations,
  cSelectFeature = "gene",
  lGetGRangesInsteadOfListCounts = FALSE,
  lGetPropInsteadOfCounts = FALSE,
  grangesData = myBam_GRanges,
  cWhichStrandVsFeaturePos = "both",
  nWindowSizeAroundFeaturePos = 600,
  lAddCorrectedDistFrom5pTo3p = TRUE,
  cFeaturePosNames = c("TSS", "TTS")
)

# adding new axis to plot from DrawModBasePropDistFromFeature function
AddToModBasePropDistFromFeaturePlot(
  dPosCountsDistFeatureStart = myCountsDist_List_bamfile[[1]],
  dPosCountsDistFeatureEnd = myCountsDist_List_bamfile[[2]],
  cSubtitleContent = "Along with nucleosome center distance (MonoNuc_3-2newreplicate)",
  cParamYLabel = "Nucleosome center count (MonoNuc_3-2newreplicate)",
  cParamColor = "cyan3",
  lAddAxisOnLeftSide = TRUE
)

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