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Compare normalized expression between two samples or groups

get_expression_scatter.Rd

Plots gene-level expression for two selected samples or group means, colours points by local density (viridis), labels the most divergent genes, and reports Pearson/Spearman correlation.

Usage

get_expression_scatter(
  x,
  sample_x,
  sample_y,
  by = c("sample", "group"),
  group_column = NULL,
  genes = NULL,
  log_transform = TRUE,
  label_top_n = 20,
  method = c("pearson", "spearman"),
  display_id = NULL
)

Arguments

x

A VISTA object.

sample_x

First sample or group to plot (character scalar).

sample_y

Second sample or group to plot (character scalar).

by

One of "sample" (use individual samples) or "group" (average replicates within group_column before plotting). Default "sample".

group_column

Column in sample_info used when by = "group" (defaults to stored grouping column).

genes

Optional character vector of genes to include; defaults to all.

log_transform

Logical; apply log2(x + 1) transform. Default TRUE.

label_top_n

Integer; number of most divergent genes to label (ranked by |x - y|). Set to 0 to disable labels.

method

Correlation method for the subtitle; "pearson" (default) or "spearman".

display_id

Optional column in rowData(x) to use for point labels (fallback to gene_id/rownames when not available).

Value

A ggplot2 object.