plot_contrast_results: Plot heatmap of contrast between two result lists

In saezlab/mistyR: Multiview Intercellular SpaTial modeling framework

Plot heatmap of contrast between two result lists

Description

Plot interexperiment contrast of views.

Usage

plot_contrast_results(
  misty.results.from,
  misty.results.to,
  views = NULL,
  cutoff.from = 1,
  cutoff.to = 1,
  trim = -Inf,
  trim.measure = c("gain.R2", "multi.R2", "intra.R2", "gain.RMSE", "multi.RMSE",
    "intra.RMSE")
)

Arguments

misty.results.from, misty.results.to	a results list generated by collect_results().
views	one or more abbreviated names of views.
cutoff.from, cutoff.to	importance thresholds respective to the result lists.
trim	display targets with performance value above (if R2 or gain) or below (otherwise) this value only.
trim.measure	the measure used for trimming.

Details

The heatmaps show the interactions that are present and have importance above a cutoff.to value in the views of misty.results.to but not present or have importance below cutoff.from in the views of misty.results.from.

Value

The misty.results.from list (invisibly).

See Also

collect_results() to generate a results list from raw results.

Other plotting functions: plot_contrast_heatmap(), plot_improvement_stats(), plot_interaction_communities(), plot_interaction_heatmap(), plot_view_contributions()

Examples

# if for example the available samples come from different grades of tumors

grade1.results <- collect_results(c("results/synthetic1", "results/synthetic2"))
grade3.results <- collect_results("results/synthetic10")

# highlight interactions present in grade 1 tumors but not in grade 3 tumors
# in the paraview

grade3.results %>% plot_contrast_results(grade1.results, views = "para.10")

# see the loss of interactions in all views with lower sensitivity

plot_contrast_results(grade3.results, grade1.results, cutoff.from = 0.75, cutoff.to = 0.5)

saezlab/mistyR documentation built on March 25, 2024, 4:12 p.m.