Plot transcripts

Source: R/transcript_model_track.R

Plot a max number of transcripts per genes. See get_tx_biotypes for a full list of all available biotypes.

transcript_model_track(
  dat,
  max_transcripts = 1,
  tx_biotypes = NULL,
  remove_pseudogenes = TRUE,
  show_plot = FALSE,
  show.legend = FALSE,
  fill = "skyblue",
  shape = c("arrow", "box", "ellipse", "smallArrow"),
  transcriptAnnotation = c("symbol", "transcript"),
  collapseTranscripts = c(FALSE, TRUE, "longest"),
  stacking = c("squish", "hide", "dense", "pack", "full"),
  method = "ggplot",
  xtext = TRUE,
  expand_x_mult = c(0.05, 0.1),
  verbose = TRUE
)

Arguments

dat

Data to query transcripts with.

max_transcripts

Maximum number of transcripts per gene.

tx_biotypes

Transcript biotypes to include in the gene model track. By default (NULL), all transcript biotypes will be included. See get_tx_biotypes for a full list of all available biotypes

remove_pseudogenes

Whether to remove known pseudogenes.

show_plot

Print plot to screen.

show.legend

Show gene plot legend.

fill

A variable name string, or a color to fill the plot data with.

shape

Shape type to plot genes as. Passed to plotTracks.

transcriptAnnotation

Whether to show the gene symbol or the full transcript ID. Passed to plotTracks.

collapseTranscripts

Logical or character scalar. Can be one in gene, longest, shortest or meta. Merge all transcripts of the same gene into one single gene model. In the case of gene (or TRUE), this will only keep the start location of the first exon and the end location of the last exon from all transcripts of the gene. For shortest and longest, only the longest or shortest transcript model is retained. For meta, a meta-transcript containing the union of all exons is formed (essentially identical to the operation reduce(geneModel)). Passed to plotTracks.

stacking

The stacking type for overlapping items of the track. One in c(hide, dense, squish, pack,full). Currently, only hide (don't show the track items, squish (make best use of the available space) and dense (no stacking at all) are implemented.

method

Method to use: "gviz" or "ggplot".

xtext

Include x-axis title and text.

expand_x_mult

Expand the x-axis limits to include partially overlapping transcripts.

verbose

Print messages.

Examples

dat <- echodata::BST1 
gene_track <- echoplot::transcript_model_track(dat=dat)
#> Converting dat to GRanges object.
#> max_transcripts= 1 . 
#> 16  transcripts from  16  genes returned.
#> Fetching data...
#> OK
#> Parsing exons...
#> OK
#> Defining introns...
#> OK
#> Defining UTRs...
#> OK
#> Defining CDS...
#> OK
#> aggregating...
#> Done
#> Constructing graphics...