ggSignalTracks: Plot genomic signal tracks with ggplot2

Usage

ggSignalTracks(
  tracks,
  region,
  ensdb = NULL,
  colors = "darkblue",
  transcripts = c("full", "collapsed", "none"),
  aggregation = c("mean+heatmap", "mean", "heatmap", "heatmap+mean"),
  extend = 0,
  showSE = FALSE,
  nbins = 1000,
  heatmap.palette = c("white", "blue", "black"),
  binSummFn = c("mean", "max"),
  sameLimits = TRUE,
  gene_label = "symbol",
  trans = c("none", "sqrt", "log1p"),
  gene_color = "black",
  baseTextSize = 9,
  xAxis = TRUE,
  coverage.linewidth = 0.2,
  verbose = TRUE
)

Arguments

tracks: A named list or named character vector, where each element is the path to one or multiple bigwig files (nesting indicates grouping).
region: The region to plot, provided either as a GRanges or character. If `ensdb` is given, `region` can also be a gene name, which will be looked up.
ensdb: An optional EnsDb object form which to grab transcripts. A `TxDb` object should also be supported.
colors: A vector of colors for each element of `tracks` (nested elements have the same colors) which will be use to color the coverage profiles. Colors will be recycled if necessary.
transcripts: Either 'full' (full transcripts plotted), 'collapsed' (to genes), or 'none'.
aggregation: How to aggregate/show nested tracks. Either 'mean', 'heatmap' (no aggregation), or 'mean+heatmap' (both, default).
extend: A numeric value indicating how much to extend beyond the `region`. If greater than 1, this indicates the number of nucleotides to add in both directions. If smaller than or equal to 1, this indicates the proportion of the region to add on both sides. Default 0.
showSE: Logical; whether to show the standard error on the coverage tracks of aggregated data.
nbins: The number of bins in which to divide the region.
heatmap.palette: A character vector specifying the colors for the heatmap. If of length 1, is assumed to indicate the RColorBrewer palette to use. If of length>1, the colors will be used with scale_fill_gradientn.
binSummFn: How to summarize date within a display bin. Either 'mean' (default) or 'max'.
sameLimits: Logical; should the tracks have the same y-axis limits (and same color scale for heatmaps)?
gene_label: What labels to print for genes. Either "symbol", "gene_id", "tx_name", or NULL.
trans: Optional transformation of the data, either 'none' (default), 'sqrt', or 'log1p'.
gene_color: The genes' color.
baseTextSize: The base plotting text size.
xAxis: Logical; whether to plot the xAxis in the bottom panel.
coverage.linewidth: Line width of the coverage plots (above ribbons).
verbose: Logical; whether to print progress messages.

Examples

# we create dummy data
bw1 <- tempfile(fileext=".bw")
cov1 <- GRanges("chr1", IRanges(1L+round(c(500+rnorm(15, sd=20),
                                           1000*runif(20))), width=30))
bw2 <- tempfile(fileext=".bw")
cov2 <- GRanges("chr1", IRanges(1L+abs(round(c(490+rnorm(15, sd=30),
                                               1000*runif(20)))), width=30))
seqlengths(cov1) <- seqlengths(cov2) <- c("chr1"=1500)
rtracklayer::export.bw(coverage(cov1), bw1)
rtracklayer::export.bw(coverage(cov2), bw2)
# then we create the ggplots, and plot them:
pl <- ggSignalTracks(list(group=c(rep1=bw1, rep2=bw2)), region="chr1:1-1030",
                     aggregation="heatmap+mean")
#> Loading BigWig data...
#>   Importing: /tmp/RtmpROo5oN/file1bcb42a605bd.bw
#>   Importing: /tmp/RtmpROo5oN/file1bcb24598b72.bw
patchwork::wrap_plots(pl, ncol=1, heights=c(2,1))