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Plot Log2 Fold-Changes of a Gene and Its Isoforms

Source: R/plot_log2fc.R
plot_log2fc.Rd

Bar plot of the log2 fold-change of one or more genes next to the fold-changes of each of their transcripts, coloured by transcript type and faded when not significant. With several genes, one panel per gene is drawn. The IsoformicExperiment method uses the stored differential expression results (see de_table()); the data frame method accepts the long table produced by de_table() or join_DEG_DET().

Usage

plot_log2fc(
  self,
  feature,
  feature_column = "gene_name",
  color_palette = NULL,
  ncol = NULL,
  ...
)

plot_log2FC(
  de_data,
  feature,
  feature_column = "gene_name",
  color_palette = NULL,
  ncol = NULL
)

Arguments

self

An IsoformicExperiment or a long DE table.

feature

Character vector of gene names (or IDs, or transcript names, matched against feature_column).

feature_column

Column of the DE table used to select features (default "gene_name").

color_palette

Named colour vector per transcript type; defaults to the object's palette or tx_type_palette().

ncol

Number of facet columns, NULL for automatic.

...

Passed on to methods.

de_data

A long DE table (see de_table()).

Value

A ggplot object.

Examples

iso <- example_isoformic()
plot_log2fc(iso, feature = "RBPJ")

plot_log2fc(iso, feature = c("RBPJ", "EGFR", "PNCK"), ncol = 1)


# Table-based
plot_log2fc(de_table(iso), feature = "RBPJ")