Scatterplot module

mod_scatterplot is a Shiny module prepared to display a scatterplot of two biomarkers with different levels of grouping. It also includes a set of listings with information about the population and the regression and correlation estimates.

Input dataframes:

bm_dataset

It expects a dataset similar to https://www.cdisc.org/kb/examples/adam-basic-data-structure-bds-using-paramcd-80288192 , 1 record per subject per parameter per analysis visit

It expects, at least, the columns passed in the parameters, subjid_var, cat_var, par_var, visit_var and value_var. The values of these variables are as described in the CDISC standard for the variables USUBJID, PARCAT, PARAM, AVISIT and AVAL.

group_dataset

It expects a dataset with an structure similar to https://www.cdisc.org/kb/examples/adam-subject-level-analysis-adsl-dataset-80283806 , one record per subject

It expects to contain, at least, subjid_var

Usage

scatterplot_UI(id)

scatterplot_server(
  id,
  bm_dataset,
  group_dataset,
  dataset_name = shiny::reactive(character(0)),
  cat_var = "PARCAT",
  par_var = "PARAM",
  value_vars = c("AVAL", "PCHG"),
  visit_var = "AVISIT",
  subjid_var = "SUBJID",
  default_x_cat = NULL,
  default_x_par = NULL,
  default_x_value = NULL,
  default_x_visit = NULL,
  default_y_cat = NULL,
  default_y_par = NULL,
  default_y_value = NULL,
  default_y_visit = NULL,
  default_group = NULL,
  default_color = NULL,
  compute_lm_cor_fn = sp_compute_lm_cor_default
)

mod_scatterplot(
  module_id,
  bm_dataset_name,
  group_dataset_name,
  cat_var = "PARCAT",
  par_var = "PARAM",
  value_vars = c("AVAL", "PCHG"),
  visit_var = "AVISIT",
  subjid_var = "SUBJID",
  default_x_cat = NULL,
  default_x_par = NULL,
  default_x_value = NULL,
  default_x_visit = NULL,
  default_y_cat = NULL,
  default_y_par = NULL,
  default_y_value = NULL,
  default_y_visit = NULL,
  default_group = NULL,
  default_color = NULL,
  compute_lm_cor_fn = sp_compute_lm_cor_default,
  bm_dataset_disp,
  group_dataset_disp
)

Arguments

id

Shiny ID [character(1)]

bm_dataset, group_dataset

[data.frame()]

Dataframes as described in the Input dataframes section

dataset_name

[shiny::reactive(*)]

a reactive indicating when the dataset has possibly changed its columns

cat_var, par_var, visit_var

[character(1)]

Columns from bm_dataset that correspond to the parameter category, parameter and visit

value_vars

[character(n)]

Columns from bm_dataset that correspond to values of the parameters

subjid_var

[character(1)]

Column corresponding to subject ID

default_x_cat, default_x_par, default_x_visit, default_x_value, default_y_cat, default_y_par

[character(1)|NULL]

Default values for the selectors

default_y_visit, default_y_value, default_group, default_color

[character(1)|NULL]

Default values for the selectors

compute_lm_cor_fn

[function()]

Function used to compute the linear regression model and correlation statistics, please view the corresponding vignette for more details.

module_id

[character(1)]

Module Shiny id

bm_dataset_name, group_dataset_name

[character(1)]

Name of the dataset

bm_dataset_disp, group_dataset_disp

[mm_dispatcher(1)]

Dataset dispatcher. This parameter is incompatible with its *_dataset_name counterpart. Only for advanced use.

Functions

• scatterplot_UI(): UI

• scatterplot_server(): Server