transcript_model_track: Plot transcripts

In bschilder/echoplot: echoverse module: Locus plot creation for fine-mapping and colocalization studies

Plot transcripts

Description

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

Usage

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.

Source

ensembld tutorial Gvix tutorial ggbio tutorial

Examples

dat <- echodata::BST1 
gene_track <- echoplot::transcript_model_track(dat=dat)

bschilder/echoplot documentation built on Oct. 26, 2023, 6:55 p.m.