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.
plot_distribution_pTAI_qqplot(
phyex_set,
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
)A ggplot2 object showing a qqplot of partial TAI distributions
A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet).
An integer specifying the index of the reference developmental stage. The partial TAI distribution of this stage will be used as the reference for comparisons with other stages (default: stage index 1).
Label of x-axis.
Label of y-axis.
Figure title.
Transparency of the points.
Size of the points.
Filipa Martins Costa