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Plot gene positions along chromosomes using a TxDb

get_chromosome_plot.Rd

Retrieves gene coordinates on the fly from a user-supplied TxDb and plots selected genes along chromosomes, optionally colouring by a numeric value and labeling the most variable genes.

Usage

get_chromosome_plot(
  x,
  txdb,
  keytype = "GENEID",
  id_column = NULL,
  genes = NULL,
  value_column = NULL,
  comparison = NULL,
  group_value = NULL,
  label_top_n = 20,
  display_id = NULL,
  line_length = 0.02,
  line_width = 0.6,
  filter_chrom = NULL,
  value_label = NULL,
  use_data_range = FALSE,
  force_fc_limits = FALSE,
  scale_mode = c("diverging", "sequential"),
  scale_low = NULL,
  scale_mid = NULL,
  scale_high = NULL,
  scale_midpoint = 0
)

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).

value_column

Optional column in rowData(x) used for colouring.

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).

group_value

Optional group label (from group_column); when supplied, uses mean expression for that group for colouring (assay norm_counts).

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_label

Optional legend title override for the colour scale.

scale_mode

Colour scale mode: "diverging" (default) or "sequential".

scale_low

Optional low-end colour override.

scale_mid

Optional midpoint colour override (used with diverging scale).

scale_high

Optional high-end colour override.

scale_midpoint

Numeric midpoint passed to ggplot2::scale_color_gradient2() when scale_mode = "diverging".

Value

A ggplot2 object.

Details

The genes argument is only used as an explicit label set (all genes are still plotted). Values in genes must match either the rownames of x or the values in id_column when that is supplied. For example, if id_column = "ENTREZID", then genes should contain Entrez IDs to be labeled. When multiple comparisons are supplied, value_column and group_value are ignored and the plot is facetted by comparison with a fixed +/-2 log2FC scale.