plot_gene: Plot abundances for all isoforms of a specified gene.
In bartongroup/RATS: Relative Abundance of Transcripts

plot_gene

R Documentation

Plot abundances for all isoforms of a specified gene.

Description

Boxplot of absolute and relative abundances for the isoforms of a given gene. The style option allows grouping by condition or by isoform.

Usage

plot_gene(
  dtuo,
  pid,
  style = "bycondition",
  fillby = NA_character_,
  colourby = NA_character_,
  shapeby = NA_character_,
  isofcolvec = c("tomato", "lightblue", "forestgreen", "purple", "hotpink", "gold3"),
  dtucolvec = c(`TRUE` = "firebrick1", `FALSE` = "dodgerblue", `NA` = "gold"),
  condcolvec = c("grey15", "steelblue"),
  replcolvec = c("red", "blue", "green", "violet", "pink", "orange"),
  nonecol = "grey50"
)

Arguments

`dtuo`	A DTU object.
`pid`	A `parent_id` to make the plot for.
`style`	Different themes: "byisoform" - Grouped by isoform. Show individual measurements as points., "bycondition" - (Default) Grouped by condition. Connect individual measurements with colour-coded lines. "lines" - Grouped by condition. Connect replicate measurements as colour-coded lines. Hide the boxplots.
`fillby`	Applies to the boxplots. Not all options will work with all styles. "isoform" - Colour fill by isoform., "condition" - Colour fill by condition., "DTU" - Colour fill by transcript-level DTU result., "none" - Uniform fill.
`colourby`	Applies to boxplot outline and points. Not all options will work with all styles. "replicate" - Point shape by replicate., "isoform" - Colour lines by isoform., "condition" - Colour lines by condition., "DTU" - Colour lines by transcript-level DTU result., "none" - Uniform colour.
`shapeby`	Applies to points. "replicate" - Point shape by replicate., "isoform" - Point shape by isoform., "condition" - Point shape by condition., "DTU" - Point shape by transcript-level DTU result., "none" - Uniform shape.
`isofcolvec`	Colour vector for isoform highlighting. Used to build a colorRampPalette.
`dtucolvec`	Colour vector for DTU highlighting.
`condcolvec`	Colour vector for condition highlighting.
`replcolvec`	Colour vector for replicate highlighting. Used to build a colorRampPalette.
`nonecol`	Colour to use when no colour coding is wanted.