Extact PVDs from pickle file

Usage

extract_figs_from_pickle(
  n_s = 1,
  dataset_name = "sample_data",
  output_folder = "output",
  rda_filename = "data.RData",
  picklename = paste0(dataset_name, "_subtype", n_s - 1, ".pickle"),
  use_rds = TRUE,
  ...
)

Arguments

n_s

helps construct picklename by identifying number of latent subgroups

dataset_name

root name of dataset

output_folder

where to find the dataset

rda_filename

name of rda file containing environment used to run analyses

picklename

the name of the pickle file to open

use_rds

logical whether to use previously cached results

...

Arguments passed on to plot_positional_var

samples_sequence: todo
samples_f: todo
n_samples: todo
score_vals: todo
biomarker_labels: todo
ml_f_EM: todo
cval: todo
subtype_order: todo
biomarker_order: todo
title_font_size: todo
stage_font_size: todo
stage_label: todo
stage_rot: todo
stage_interval: todo
label_font_size: todo
label_rot: todo
cmap: a character
biomarker_colours: a character vector of colors
subtype_titles: todo
separate_subtypes: todo
save_path: todo
save_kwargs: todo
results: todo
biomarker_levels: doesn't do much right now
biomarker_groups: biomarker groupings
biomarker_events_table: todo
biomarker_event_names: todo
biomarker_plot_order: todo
synchronize_y_axes: todo

Value

a "PVD.list (a list of PVD objects from autoplot.PF())

Examples

output_path <-
  fs::path_package("extdata/sim_data", package = "fxtas")

if (dir.exists(output_path)) {
  figs <- extract_figs_from_pickle(
    output_folder = output_path,
    n = 3
  )

  figs
}
#> $`Group 1`

#> 
#> $`Group 2`

#> 
#> $`Group 3`

#> 
#> attr(,"class")
#> [1] "PVD.list" "list"    
#> attr(,"biomarker_event_names")
#>  [1] "Biomarker 1: 1" "Biomarker 2: 1" "Biomarker 3: 1" "Biomarker 4: 1"
#>  [5] "Biomarker 5: 1" "Biomarker 1: 2" "Biomarker 2: 2" "Biomarker 3: 2"
#>  [9] "Biomarker 4: 2" "Biomarker 5: 2" "Biomarker 1: 3" "Biomarker 2: 3"
#> [13] "Biomarker 3: 3" "Biomarker 4: 3" "Biomarker 5: 3"