Tutorial: drug_regimen_sunburst

Introduction

The drug_regimen_sunburst() function allows the user to visualize the complete treatment course for selected diagnoses in a given analytic cohort. The function returns a list containing a ‘treatment_history’ data frame and the interactive plot ‘sunburst_plot’.

Modifying Function Arguments

`drug_regimen_sunburst()` Function Arguments
Argument Description

data_synapse

 The item from the nested list returned from pull_data_synapse() corresponding to the cancer cohort of interest.

data_cohort

 The list returned from the `create_analytic_cohort()` function call.

max_n_regimens

 The number of lines of treatment displayed in the sunburst plot.

Note that the innermost circle of the sunburst plot indicates the first therapies that patients received following diagnosis. The circle is divided proportionally based on the percentage of patients that received a particular treatment. Each subsequent ring of the sunburst corresponds to a subsequent treatment regimen, such that the inner rings represent earlier treatments. Together, the rings illustrate the distribution and patterns of various treatment regimens.

Setup

Before going through the tutorial, load the {genieBPC} library and log into Synapse using the set_synapse_credentials() function. For more information on set_synapse_credentials(), refer to the Tutorial: pull_data_synapse() vignette.

library(genieBPC)

set_synapse_credentials()

This tutorial will utilize the data downloaded in the Tutorial: pull_data_synapse() vignette, as shown below:

nsclc_2_0 = pull_data_synapse("NSCLC", version = "v2.0-public")

Example

The example below creates a sunburst plot of the first three cancer-directed regimens received by patients diagnosed with Stage IV NSCLC.

nsclc_stg_iv = create_analytic_cohort(data_synapse = nsclc_2_0$NSCLC_v2.0,
                                      stage = c("Stage IV"))

nsclc_treatment = drug_regimen_sunburst(data_synapse = nsclc_2_0$NSCLC_v2.0,
                      data_cohort = nsclc_stg_iv,
                      max_n_regimens = 3)
head(nsclc_treatment$treatment_history)
#> # A tibble: 6 x 2
#>   path                                                                       Pop
#>   <chr>                                                                    <int>
#> 1 Afatinib Dimaleate                                                           1
#> 2 Afatinib Dimaleate-Afatinib Dimaleate, Carboplatin, Pemetrexed Disodium~     1
#> 3 Afatinib Dimaleate-Cisplatin, Pemetrexed Disodium-Osimertinib                1
#> 4 Afatinib Dimaleate-Erlotinib Hydrochloride-Bevacizumab, Carboplatin, Pe~     1
#> 5 Afatinib Dimaleate-Erlotinib Hydrochloride-Investigational Drug              1
#> 6 Afatinib Dimaleate-Gefitinib-Bevacizumab, Carboplatin, Pemetrexed Disod~     1
nsclc_treatment$sunburst_plot
Legend