DrawModLogo: DrawModLogo Function (GloModAn)

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

DrawModLogo Function (GloModAn)

Description

Return a plot describing the sequence motif associated to the sequences provided. Sequences that do not have full width and sequences that have some N or some gaps "-" are automatically removed before drawing the sequence plot.

Usage

DrawModLogo(
  dnastringsetSeqAroundMod,
  nGenomicBgACGT = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
  cYunit = "ic_hide_bg",
  lPlotNegYAxis = TRUE,
  cColorsACGT = c(A = "#4daf4a", C = "#377eb8", G = "#ffd92f", T = "#e41a1c"),
  nPositionsToAnnotate = NULL,
  cAnnotationText = NULL,
  nTagTextFontSize = 20,
  lXAxis = TRUE,
  lYAxis = TRUE,
  nXFontSize = 15,
  nYFontSize = 15
)

Arguments

dnastringsetSeqAroundMod	A DNAStringSet object containing the sequence around each DNA modification. All these sequences must have the same size and the modification must have the same position in each sequence (e.g. at the center).
nGenomicBgACGT	A numeric vector giving the background to be corrected with the genomic composition in Adenine (A) then Cytosine (C) then Guanine (G) then Thymine (T). Defaults to c(A=0.25, C=0.25, G=0.25, T=0.25).
cYunit	Units to be used for the y axis. Can be "ic" (information content), "ic_hide_bg" (information content + hide low signal) or "prob" (probability). "ic_hide_bg" will hide the letters on the upper panel (OR the lower panel) if these letters have probabilities above (OR below) the background signal based on the genomic composition. Defaults to "ic_hide_bg".
lPlotNegYAxis	If TRUE, allow plotting the lower panel to show depletion among the sequences provided. Defaults to TRUE.
cColorsACGT	A character vector giving the color for the Adenine (A) then Cytosine (C) then Guanine (G) then Thymine (T) letters on the plot. Defaults to c(A="red2", C="blue2", G="orange2", T="green3").
nPositionsToAnnotate	A numeric vector giving the positions to highlight on the logo using small triangular tags (e.g. DNA modifications on a fixed position). Defaults to NULL.
cAnnotationText	A character vector. If nPositionsToAnnotate is not NULL, this option can provide labels to be associated to each annotation tag. If the vector's length is 1, it will be used for all tags to be displayed. Defaults to NULL.
nTagTextFontSize	Font size for the text associated to the annotation tags. Defaults to 20.
lXAxis	If TRUE, the x-axis is plotted. Defaults to TRUE.
lYAxis	If TRUE, the y-axis is plotted. Defaults to TRUE.
nXFontSize	Font size for the text associated to the x axis. Defaults to 15.
nYFontSize	Font size for the text associated to the y axis. Defaults to 15.

Details

This function reduce the background signal using the genomic composition and also computes the signal of depleted bases among the sequence provided. Positions that are fixed and displaying only one base are taken in account and avoid these two corrections. It is also possible to tag some positions (+/- labels) in the logo.

Examples

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

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

# Retrieve GRanges with sequence
myPositions_Mod_Granges_wSeq <- GetGRangesWindowSeqandParam(
  grangesData = myGrangesPacBioGFF,
  grangesGenome = myGrangesGenome,
  dnastringsetGenome = myGenome,
  nUpstreamBpToAdd = 5,
  nDownstreamBpToAdd = 5
)

DrawModLogo(
  dnastringsetSeqAroundMod = as(myPositions_Mod_Granges_wSeq$sequence, "DNAStringSet"),
  nGenomicBgACGT = c(0.35, 0.15, 0.15, 0.35),
  nPositionsToAnnotate = c(6), cAnnotationText = c("6mA")
)

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