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Fold-change scatterplot between two comparisons

get_foldchange_scatter.Rd

Plots log2 fold changes from two stored comparisons against each other, with points coloured by concordant/discordant regulation based on the cutoffs saved in the VISTA object.

Usage

get_foldchange_scatter(
  x,
  sample_comparisons,
  label_top_n = 0,
  point_alpha = 0.5,
  use_hex = FALSE,
  method = c("pearson", "spearman")
)

Arguments

x

A VISTA object containing DE results.

sample_comparisons

Character vector of length 2 naming the comparisons.

label_top_n

Integer; number of most extreme points to label (by |log2FC1| + |log2FC2|).

point_alpha

Point transparency.

use_hex

Logical; use hex binning instead of points for dense datasets.

method

Correlation method for the subtitle; "pearson" or "spearman".

Value

A ggplot2 object.

Details

Points are coloured by concordance status using fixed colours:

  • Up/Up = #1b9e77

  • Down/Down = #7570b3

  • Up/Down = #d95f02

  • Down/Up = #e7298a

  • Other = grey70

Regulation is derived from the log2fc and pval cutoffs stored in cutoffs(x) (and p_value_type from the same list, defaulting to "padj").