Plot exon and domain architectures

Plot exon and domain architectures

Plot exon and domain architectures

# S4 method for factR
plotTranscripts(
  object,
  ...,
  collapse = FALSE,
  rescale_introns = FALSE,
  ncol = 1
)

# S4 method for factR
plotDomains(object, ..., ncol = 1)

# S4 method for factR
plot2way(object, x, y, plot_trend = FALSE)

Arguments

object

factR object class

...

One or more features to plot. Can be the following:

  • gene_id: ID of gene to plot

  • gene_name: Name of gene to plot

  • transcript_id: ID of transcript to plot

collapse

Whether to collapse all transcripts into one (Default: FALSE)

rescale_introns

Whether to rescale intron sizes. Useful for genes with extremely long introns, this will place emphasis on the exon architectures

ncol

Dimension of patchworked plot. Applicable if 2 or more features are plotted

x

Feature to plot. Can be the following:

  • gene_id: ID of gene to plot

  • gene_name: Name of gene to plot

  • transcript_id: ID of transcript to plot

  • AS_id: ID of alternative splicing event (ASxxxxx)

  • sample: Column name from sample metadata

plot_trend

Whether to plot trendline (Default: FALSE)

Value

Interactive plotly plot

ggplot2 plot

Examples

## Load sample factRObject
data(factRsample)

## Plot transcript archtectures:
plotTranscripts(factRsample, "Dab2")


plotTranscripts(factRsample, "Dab2", collapse=TRUE)


plotTranscripts(factRsample, "Dab2", rescale_introns=TRUE)



## To plot protein-coding domains, the CDS segments need to be built first:
factRsample <- buildCDS(factRsample)
factRsample <- getAAsequence(factRsample)

## Plotting of domains:
plotDomains(factRsample, "Dab2")
#> ℹ Set `show_more to TRUE to show more info`
#> Warning: Skipped 6 non-coding transcripts
#> Warning: These transcripts are non-coding: ENSMUST00000159046.1, ENSMUST00000159490.7, ENSMUST00000159552.1, ENSMUST00000162140.1, MSTRG.14564.1, MSTRG.14566.1