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,
  biomarker_groups = readr::read_rds(fs::path(output_folder, "biomarker_groups.rds")),
  biomarker_levels = readr::read_rds(fs::path(output_folder, "biomarker_levels.rds")),
  ...
)

Arguments

n_s

number of latent subgroups; helps construct picklename

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

biomarker_groups

data.frame with group colors, etc

biomarker_levels

list containing biomarker ordinal level info

...

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_events_table: todo
biomarker_event_names: todo
biomarker_plot_order: todo
synchronize_y_axes: todo
use_labels: whether to use biomarker labels or variable names

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
}
#> $`Subtype 1`

#> 
#> $`Subtype 2`

#> 
#> $`Subtype 3`

#> 
#> attr(,"class")
#> [1] "PVD_list" "list"    
#> attr(,"biomarker_labels")
#> [1] "Biomarker 1" "Biomarker 2" "Biomarker 3" "Biomarker 4" "Biomarker 5"
#> attr(,"biomarker_event_names")
#> <labelled<character>[15]>
#>  [1] Biomarker 1: 1 Biomarker 2: 1 Biomarker 3: 1 Biomarker 4: 1 Biomarker 5: 1
#>  [6] Biomarker 1: 2 Biomarker 2: 2 Biomarker 3: 2 Biomarker 4: 2 Biomarker 5: 2
#> [11] Biomarker 1: 3 Biomarker 2: 3 Biomarker 3: 3 Biomarker 4: 3 Biomarker 5: 3
#> 
#> Labels:
#>           value          label
#>  Biomarker 1: 0 Biomarker 1: 0
#>  Biomarker 1: 1 Biomarker 1: 1
#>  Biomarker 1: 2 Biomarker 1: 2
#>  Biomarker 1: 3 Biomarker 1: 3
#>  Biomarker 2: 0 Biomarker 2: 0
#>  Biomarker 2: 1 Biomarker 2: 1
#>  Biomarker 2: 2 Biomarker 2: 2
#>  Biomarker 2: 3 Biomarker 2: 3
#>  Biomarker 3: 0 Biomarker 3: 0
#>  Biomarker 3: 1 Biomarker 3: 1
#>  Biomarker 3: 2 Biomarker 3: 2
#>  Biomarker 3: 3 Biomarker 3: 3
#>  Biomarker 4: 0 Biomarker 4: 0
#>  Biomarker 4: 1 Biomarker 4: 1
#>  Biomarker 4: 2 Biomarker 4: 2
#>  Biomarker 4: 3 Biomarker 4: 3
#>  Biomarker 5: 0 Biomarker 5: 0
#>  Biomarker 5: 1 Biomarker 5: 1
#>  Biomarker 5: 2 Biomarker 5: 2
#>  Biomarker 5: 3 Biomarker 5: 3
#> attr(,"biomarker_groups")
#> # A tibble: 5 × 3
#>   biomarker   biomarker_group group_color
#> * <chr>       <chr>           <chr>      
#> 1 Biomarker 1 group 1         #88CCEE    
#> 2 Biomarker 2 group 1         #88CCEE    
#> 3 Biomarker 3 group 2         #CC6677    
#> 4 Biomarker 4 group 2         #CC6677    
#> 5 Biomarker 5 group 3         #888888    
#> attr(,"biomarker_levels")
#> $`Biomarker 1`
#> [1] 0 1 2 3
#> 
#> $`Biomarker 2`
#> [1] 0 1 2 3
#> 
#> $`Biomarker 3`
#> [1] 0 1 2 3
#> 
#> $`Biomarker 4`
#> [1] 0 1 2 3
#> 
#> $`Biomarker 5`
#> [1] 0 1 2 3
#> 
#> attr(,"class")
#> [1] "levels_list" "list"