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Comparing expression levels distributions across developmental stages

Source: R/plot_distribution_expression.R
plot_distribution_expression.Rd

plot_distribution_expression generates plots that help to compare the distribution of expression levels through various developmental stages or cell types, highlighting each stage with distinct colors. By default, a log transformation is applied to the expression values.

Usage

plot_distribution_expression(
  phyex_set,
  show_identities = TRUE,
  show_strata = FALSE,
  log_transform = TRUE,
  seed = 123
)

Arguments

phyex_set

A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet).

show_identities

Logical, whether to show identity-specific distributions.

show_strata

Logical, whether to show stratum-specific distributions.

log_transform

Logical, whether to apply log transformation to expression values (default: TRUE).

seed

Seed for reproducible color selection.

Recommendation

Apply a square root transformation to enhance the visualization of differences in the distributions: plot_distribution_expression(transform_counts(phyex_set, sqrt))

Author

Filipa Martins Costa