Prepare for BEAM plotting

Add a "plot" column to beam.specs, which includes string of plot commands.

Usage

prep_beam_plot(beam.data, beam.specs)

Arguments

beam.data

Result of prep.beam.data

beam.specs

A data.frame of strings with columns name, mtx, mdl (string with R model with mtx.row)

Value

An updated beam.specs object that includes the column "plot"

Examples

data(clinf)
data(omicdat)
data(omicann)
data(setdat)
test.beam.data <- prep_beam_data(main.data=clinf, mtx.data=omicdat,
                                 mtx.anns=omicann, set.data=setdat,
                                 set.anns=NULL, n.boot=10, seed=123)
#> Checking inputs: Tue Jul 30 13:51:24 2024
#>   Checking that each element of mtx.data is a matrix: Tue Jul 30 13:51:24 2024
#>   Checking that each element of mtx.anns is a data.frame: Tue Jul 30 13:51:24 2024
#> Aligning main.data with each mtx.data: Tue Jul 30 13:51:24 2024
#>   Working on mtx.data Lesion (1 of 2): Tue Jul 30 13:51:24 2024
#>   Working on mtx.data RNA (2 of 2): Tue Jul 30 13:51:24 2024
#> Warning: Some ids not matched; returning NAs for those.
#>   Working on mtx.anns: Tue Jul 30 13:51:24 2024
#>   Matching matrix 1 with annotations: Tue Jul 30 13:51:24 2024
#>   Matching matrix 2 with annotations: Tue Jul 30 13:51:24 2024
#>   Checking set.data: Tue Jul 30 13:51:24 2024
#>     Ordering and indexing set.data: Tue Jul 30 13:51:24 2024
#>     Checking section 1 of 40 of set.data: Tue Jul 30 13:51:24 2024
#> Generating bootstrap index matrix: Tue Jul 30 13:51:24 2024
#> Packaging and returning result: Tue Jul 30 13:51:24 2024
specs <- prep_beam_specs(beam.data=test.beam.data, endpts=c("MRD29", "EFS", "OS"),
                         firth=TRUE)
#> MRD29 is continuous, fitting lm
#> EFS is survival endpoint, fitting coxphf2
#> OS is survival endpoint, fitting coxphf2
plot.specs <- prep_beam_plot(beam.data=test.beam.data, beam.specs=specs)