TrackPlot

Source code

Description

Plot read/UMI coverage and transcript tracks from BAM(s).

Usage

TrackPlot(
  bamfile = NULL,
  chr = NULL,
  start = NULL,
  end = NULL,
  gene = NULL,
  strand = c("both", "forward", "reverse", "ignore"),
  split.bc = FALSE,
  bin = 1000,
  cell.tag = "CB",
  umi.tag = "UB",
  gtf = NULL,
  max.depth = 0,
  group.title.size = rel(2),
  cell.group = NULL,
  display.genes = NULL,
  meta.features = NULL,
  log.scaled = FALSE,
  upstream = 1000,
  downstream = 1000,
  fragfile = NULL,
  atac.log.scaled = FALSE,
  atac.max.depth = 0,
  col.by = NULL,
  layout.heights = c(1, 10, 2),
  highlights = NULL,
  junc = FALSE,
  junc.min.depth = 5
)

Arguments

bamfile A path to a BAM file or a list to BAM files. BAM file(s) should be indexed.
chr Chromosome name.
start Start position.
end End position.
strand Plot reads on strand. Default is bot strands. Can be one of c(“both”, “forward”, “reverse”, “ignore”). When set to ignore, read strand information will be discarded.
split.bc Split coverage by barcode. Default is FALSE, bulk mode.
bin Divide plot region into bins. Save plot time. Default is 1000.
cell.tag Tag for cell barcode in the BAM. Default is “CB”.
umi.tag Tag for UMI in the BAM. Default is “UB”.
gtf GTF database, load by gtf2db.
max.depth Max depth capped to plot. Default is 0, no capping.
group.title.size Font size for track group titles. Default is rel(2).
cell.group Vector or list of cell group IDs. Name for the ID is the cell name. If bamfile is a list, the cell.group can also be a list with the same length of bamfile list, and binding cell.group to bam file by the name or order in both lists. See manual online for real cases. <https://shiquan.github.io/Yano.html>
display.genes Vector of genes to plot in the target region. Other genes in this region will not print in transcript track plot.
meta.features Meta table for features. If set the regions will be also plot on top of track plot. Meta table can be accessed by object[[assay]][[]].
log.scaled Log scaled the coverage depth per group. Only used if the depth is super high. Disabled in default.
upstream Flank the target region with upstream to plot. Default is 1000.
downstream Flank the target region with downstream to plot. Default is 1000.
fragfile Fragment file for ATAC data.
atac.log.scaled Log scaled the coverage depth per group for ATAC tracks.
atac.max.depth Capped depth to plot for ATAC tracks.
col.by Color bed regions by value. The specified name should be a colname in meta table. Only support discrete value.
layout.heights Layout for track plots. Default is c(10,2) or c(1,10,2) if meta.features specified or c(1,10,10,2) if fragment file also specified.
highlights A region of a list of regions to hightlight. The region is format as c(start,end).
junc Also plot the junction reads.
junc.min.depth Filter out junctions if low than this cutoff. This parameter used to remove noise background. Default is 5.
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