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Generate BEAM Plot List

Source: R/gen_beam_plot_list.R
gen_beam_plot_list.Rd

Internal function: generate a list of clinical feature plots.

Usage

gen_beam_plot_list(
  beam.result,
  beam.specs,
  beam.feat.pvals,
  number.pairs = 1,
  set.id,
  feat.id = NULL,
  title.size = 10,
  pair.order = "both",
  endpt.order = NULL
)

Arguments

beam.result

Result of prep.beam.data

beam.specs

A data.frame of strings with columns name, mtx, mdl, plot

beam.feat.pvals

List of feature-level p-values from compute_feature_pvalues

number.pairs

Numeric; number of features to display in clinical plots, ordered by significance

set.id

A character with set name; must be in beam.result$beam.data$set.data$set.id

feat.id

Default NULL; a character with feature name; must be in beam.result$beam.data$set.data$row.id

title.size

A numeric. Specify the size of individual plot titles. Default is 10.

pair.order

One of c("both", "omic", "endpoint"). Default is "both." Specify how to choose feature-endpoint plots to include. If "both", find the best (based on q, p, effect size) feature-omic pair for each type of omic and each endpoint separately. If "omic", within each omic, find the best feature-endpoint pair and then plot this feature with all endpoints. If "endpoint", need to specify endpt.order as the name of chosen endpoint. Then, within each omic, find the feature with best association with the selected endpoint, and plot this feature for all endpoints.

endpt.order

Default NULL. If pair.order="endpoint", specify character with endpoint name (from beam.specs$name, after the period).

Value

A list of plots for the specified set and/or feature.

Examples

data(beam_stats)
test.feat.pvals <- compute_feature_pvalues(beam.stats=beam_stats)
#> Computing feature p-values for stat matrix 1 of 6: Tue Jul 30 13:51:20 2024
#>   This matrix has 20 features.
#> Computing feature p-values for stat matrix 2 of 6: Tue Jul 30 13:51:20 2024
#>   This matrix has 20 features.
#> Computing feature p-values for stat matrix 3 of 6: Tue Jul 30 13:51:20 2024
#>   This matrix has 20 features.
#> Computing feature p-values for stat matrix 4 of 6: Tue Jul 30 13:51:20 2024
#>   This matrix has 20 features.
#> Computing feature p-values for stat matrix 5 of 6: Tue Jul 30 13:51:20 2024
#>   This matrix has 20 features.
#> Computing feature p-values for stat matrix 6 of 6: Tue Jul 30 13:51:20 2024
#>   This matrix has 20 features.
plot.specs <- prep_beam_plot(beam.data=beam_stats$beam.data,
                             beam.specs=beam_stats$beam.specs)
plot.list <- gen_beam_plot_list(beam.result=beam_stats, beam.specs=plot.specs,
                                beam.feat.pvals=test.feat.pvals,
                                number.pairs=1, set.id="ENSG00000099810",
                                feat.id=NULL, title.size=11,
                                pair.order="omic", endpt.order=NULL)