plotAllelicGene: Plot allelic counts in a gene context using Gviz

In mikelove/fishpond: Fishpond: downstream methods and tools for expression data

Plot allelic counts in a gene context using Gviz

Description

Plot allelic data (allelic proportions, isoform propostions) in a gene context leveraging the Gviz package. See the allelic vignette for example usage. TPM and count filters are used by default to clean up the plot of features with minimal signal; note that the isoform proportion displayed at the bottom of the plot is among the features that pass the filtering steps. If the function is not responding, it is likely due to issues connecting to UCSC servers to draw the ideogram, in this case set ideogram=FALSE.

Usage

plotAllelicGene(
  y,
  gene,
  db,
  region = NULL,
  symbol = NULL,
  genome = NULL,
  tpmFilter = 1,
  isoPropFilter = 0.05,
  countFilter = 10,
  pc = 1,
  transcriptAnnotation = "symbol",
  labels = list(a2 = "a2", a1 = "a1"),
  qvalue = TRUE,
  log2FC = TRUE,
  ideogram = FALSE,
  cov = NULL,
  covFacetIsoform = FALSE,
  allelicCol = c("dodgerblue", "goldenrod1"),
  isoformCol = "firebrick",
  statCol = "black",
  gridCol = "grey80",
  baselineCol = "black",
  titleCol = "black",
  titleAxisCol = "black",
  titleBgCol = "white",
  geneBorderCol = "darkblue",
  geneFillCol = "darkblue",
  genomeAxisCol = "black",
  innerFontCol = "black",
  ...
)

Arguments

y	a SummarizedExperiment (see swish)
gene	the name of the gene of interest, requires a column gene_id in the metadata columns of the rowRanges of y
db	either a TxDb or EnsDb object to use for the gene model
region	GRanges, the region to be displayed in the Gviz plot. if not specified, will be set according to the gene plus 20 of the total gene extent on either side
symbol	alternative to gene, to specify the gene of interest according to a column symbol in the metadata columns of the rowRanges of y
genome	UCSC genome code (e.g. "hg38", if not specified it will use the GenomeInfoDb::genome() of the rowRanges of y
tpmFilter	minimum TPM value (mean over samples) to keep a feature
isoPropFilter	minimum percent of isoform proportion to keep a feature
countFilter	minimum count value (mean over samples) to keep a feature
pc	pseudocount to avoid dividing by zero in allelic proportion calculation
transcriptAnnotation	argument passed to Gviz::GeneRegionTrack ("symbol", "gene", "transcript", etc.)
labels	list, labels for a2 (non-effect) and a1 (effect) alleles
qvalue	logical, whether to inclue qvalue track
log2FC	logical, whether to include log2FC track
ideogram	logical, whether to include ideogram track
cov	character specifying a factor or integer variable to use to facet the allelic proportion plots, should be a column in colData(y)
covFacetIsoform	logical, if cov is provided, should it also be used to facet the isoform proportion track, in addition to the allelic proportion track
allelicCol	the colors of the points and lines for allelic proportion
isoformCol	the colors of the points and lines for isoform proportion
statCol	the color of the lollipops for q-value and log2FC
gridCol	the color of the grid in the data tracks
baselineCol	the color of the horizontal baseline for q-value and lo2gFC
titleCol	font color of the side titles (track labels)
titleAxisCol	axis color of the side titles (track labels)
titleBgCol	background color of the side titles (track labels)
geneBorderCol	the color of the borders and font in gene region track
geneFillCol	the color of the fill in the gene region track
genomeAxisCol	line color of the genome axis track
innerFontCol	font color of genome axis track, ideogram, and allelic proportion legend
...	additional arguments passed to Gviz::plotTracks()

Value

nothing, a plot is displayed

References

The methods for allelic expression analysis are described in:

Euphy Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro, Michael I. Love. "Detecting isoform-level allelic imbalance accounting for inferential uncertainty" bioRxiv (2022) https://doi.org/10.1101/2022.08.12.503785

This function makes use of the Gviz package that is described in:

Hahne, F., Ivanek, R. (2016). Visualizing Genomic Data Using Gviz and Bioconductor. In: Mathé, E., Davis, S. (eds) Statistical Genomics. Methods in Molecular Biology, vol 1418. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3578-9_16

mikelove/fishpond documentation built on Aug. 29, 2023, 2:45 p.m.