Skip to contents

Generate MA plot from a VISTA object

get_ma_plot.Rd

Create an MA plot (log2 fold change vs mean expression) for a selected comparison contained in a VISTA object. Genes are coloured by their regulation class and the top results can be optionally labeled with gene IDs.

Usage

get_ma_plot(
  x,
  sample_comparison,
  point_size = 1.2,
  alpha = 0.6,
  fill_colors = c(Up = "#a40000", Down = "#16317d", Other = "gray70"),
  topn = 0,
  label_size = 3,
  repair = FALSE,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL
)

Arguments

x

A VISTA object.

sample_comparison

Character scalar naming the comparison to plot. Must match one of names(comparisons(x)).

point_size

Numeric point size. Default: 1.2.

alpha

Numeric transparency (0-1). Default: 0.6.

fill_colors

Named character vector of colors for "Up", "Down", and "Other" genes.

topn

Integer number of genes to label. Default: 0.

label_size

Text size for labels. Default: 3.

repair

Logical; if TRUE, attempt to shorten gene identifiers to symbols by stripping prefixes. Default: FALSE.

display_id

Optional ID/column name to use for labels. If supplied and present in rowData(x), those values are used; otherwise falls back to ID mapping.

display_from

Optional source ID type for mapping (used when display_id is not found in rowData).

display_orgdb

Optional OrgDb used for ID mapping when display_id is set but not found in rowData.

Value

A ggplot MA plot.