plot_distribution_partialTAI_qqplot: QQ plot comparing partial TAI distributions across...

In drostlab/myTAI: Evolutionary Transcriptomics

QQ plot comparing partial TAI distributions across developmental stages against a reference stage

Description

plot_distribution_partialTAI_qqplot generates a QQ plot to compare the partial TAI distributions of various developmental stages against a reference stage. It visualizes quantile differences between the reference and other stages, highlights each stage with distinct colors, and annotates the plot with the p-values from the nonparametric ks.test to indicate the significance of distribution differences.

Usage

plot_distribution_partialTAI_qqplot(
  ExpressionSet,
  reference_stage_index = 1,
  xlab = "Quantiles of Reference Stage",
  ylab = "Quantiles of Other Stages",
  main = "QQ Plot: Developmental Stages vs Reference Stage (p-values from KS test)",
  alpha = 0.7,
  size = 1.2
)

Arguments

ExpressionSet	a standard PhyloExpressionSet or DivergenceExpressionSet object.
reference_stage_index	an integer specifying the index of the reference developmental stage of the ExpressionSet. The partial TAI distribution of this stage will be used as the reference for comparisons with other stages (as default stage index 1).
xlab	label of x-axis.
ylab	label of y-axis.
main	figure title.
alpha	transparency of the point.
size	size of the points.

Author(s)

Filipa Martins Costa

drostlab/myTAI documentation built on June 13, 2025, 6:24 a.m.