Visualize drug regimen sequences in a sunburst plot — drug_regimen

This function allows the user to visualize the complete treatment course for selected cancer diagnoses.

Usage

drug_regimen_sunburst(data_synapse, data_cohort, max_n_regimens = NULL, ...)

Arguments

data_synapse: The item from the nested list returned from `pull_data_synapse()`
data_cohort: The list returned from the `create_analytic_cohort()` function call
max_n_regimens: The maximum number of regimens displayed in the sunburst plot
...: Additional parameters passed to `sunburstR::sunburst()`

Value

Returns data frame `treatment_history` and interactive plot `sunburst_plot`

Details

See the drug_regimen_sunburst vignette for additional details and examples.

Examples

# Example 1 ----------------------------------
# Example using package test data
# get clinico-genomic files for a specific cohort
nsclc_sub <- create_analytic_cohort(
  data_synapse = genieBPC::nsclc_test_data,
  stage_dx = c("Stage III", "Stage IV")
)

# create sunburst plot
ex1 <- drug_regimen_sunburst(
  data_synapse = nsclc_test_data,
  data_cohort = nsclc_sub,
  max_n_regimens = 3
)

# Example 2 ----------------------------------
# using pull_data_synapse
nsclc_2_0 <- pull_data_synapse("NSCLC", version = "v2.0-public")
#> Error in .get_synapse_token(pat = pat): No credentials found. Have you authenticated yourself? Use
#> `set_synapse_credentials()` to set credentials for this session, or pass a
#> `pat` (see README:'Data Access & Authentication' for details on
#> authentication).

nsclc_stg_iv <- create_analytic_cohort(
  data_synapse = nsclc_2_0$NSCLC_v2.0,
  stage = "Stage IV"
)
#> Error: object 'nsclc_2_0' not found

ex2 <- drug_regimen_sunburst(
  data_synapse = nsclc_2_0$NSCLC_v2.0,
  data_cohort = nsclc_stg_iv,
  max_n_regimens = 3
)
#> Error: object 'nsclc_2_0' not found