Skip to contents

Chromosome plot for fold change

get_foldchange_chromosome_plot.Rd

Convenience wrapper around get_chromosome_plot() for fold-change colouring. When multiple comparisons are supplied, panels are facetted by comparison with log2FC clipped to +/-2.

Usage

get_foldchange_chromosome_plot(
  x,
  txdb,
  keytype = "GENEID",
  id_column = NULL,
  genes = NULL,
  sample_comparison = NULL,
  value_column = NULL,
  label_n = 20,
  display_id = NULL,
  line_length = 0.02,
  line_width = 0.6,
  filter_chrom = NULL
)

Arguments

x

A VISTA object.

txdb

A TxDb object (e.g., from GenomicFeatures).

keytype

Key type in the TxDb matching id_column (default "GENEID").

id_column

Optional column in rowData(x) used to match to TxDb keys. When NULL, rownames(x) are used as keys.

genes

Optional character vector of gene IDs to label (alternative to label_top_n). When provided, all genes are plotted but only these are labeled. Defaults to NULL (no explicit label set).

sample_comparison

Optional comparison name (or vector of names) used for fold-change colouring.

value_column

Optional column in rowData(x) used for colouring.

label_n

Integer; number of genes with the largest absolute fold-change to label when genes is not supplied. Set to 0 to disable labels.

display_id

Optional column in rowData(x) to use for point labels (fallback to gene_id/rownames).

line_length

Horizontal half-length (in megabases) of the tick used to mark each gene position. Default 0.02. Increase for longer ticks.

line_width

Line width of the tick marks. Default 0.6.

filter_chrom

Optional character vector of chromosomes to keep (e.g., c("chr1","chr2")). When NULL, all chromosomes returned by the TxDb are shown.

Value

A ggplot2 object.

Examples

v <- example_vista()
p <- try(get_foldchange_chromosome_plot(v, sample_comparison = names(comparisons(v))[1]), silent = TRUE)
if (!inherits(p, 'try-error')) print(p)