Chromosome plot for fold change — get_foldchange_chromosome

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,
  comparison = NULL,
  value_column = NULL,
  label_top_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).
comparison: Optional comparison name; when supplied, uses log2fc from metadata(x)$de_results[[comparison]] for colouring. If multiple comparisons are provided, one panel per comparison is shown (log2FC clipped to ±2).
value_column: Optional column in rowData(x) used for colouring.
label_top_n: Integer; number of genes with largest |value| (or random if no value) to label. Ignored when genes is provided. 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.