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Butterfly plot Teal Module

Source: R/tm_g_butterfly.R
tm_g_butterfly.Rd

Display butterfly plot as a shiny module

Usage 

tm_g_butterfly(
  label,
  dataname,
  filter_var = NULL,
  right_var,
  left_var,
  category_var,
  color_by_var,
  count_by_var,
  facet_var = NULL,
  sort_by_var = teal.transform::choices_selected(selected = "count", choices = c("count",
    "alphabetical")),
  legend_on = TRUE,
  plot_height = c(600L, 200L, 2000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  transformators = list()
)

Arguments

label

(character(1)) Label shown in the navigation item for the module or module group. For modules() defaults to "root". See Details.

dataname

(character(1))
analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().

filter_var

(choices_selected) variable name of data filter, please see details regarding expected values, default isNULL.choices vector with filter_var choices, default is NULL

right_var

(choices_selected) dichotomization variable for right side

left_var

(choices_selected) dichotomization variable for left side

category_var

(choices_selected) category (y axis) variable

color_by_var

(choices_selected) variable defines color blocks within each bar

count_by_var

(choices_selected) variable defines how x axis is calculated

facet_var

(choices_selected) variable for row facets

sort_by_var

(choices_selected) argument for order of class and term elements in table, default here is "count"

legend_on

(boolean) value for whether legend is displayed

plot_height

(numeric(3))
vector to indicate default value, minimum and maximum values.

plot_width

(numeric(3))
vector to indicate default value, minimum and maximum values.

pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

transformators

(list of teal_transform_module) that will be applied to transform module's data input. To learn more check vignette("transform-input-data", package = "teal").

Value

the teal::module() object.

Details

filter_var option is designed to work in conjunction with filtering function provided by teal (encoding panel on the right hand side of the shiny app). It can be used as quick access to predefined subsets of the domain datasets (not subject-level dataset) to be used for analysis, denoted by an value of "Y". Each variable within the filter_var_choices is expected to contain values of either "Y" or "N". If multiple variables are selected as filter_var, only observations with "Y" value in each and every selected variables will be used for subsequent analysis. Flag variables (from ADaM datasets) can be used directly as filter.

Reporting

This module returns an object of class teal_module, that contains a server function. Since the server function returns a teal_report object, this makes this module reportable, which means that the reporting functionality will be turned on automatically by the teal framework.

For more information on reporting in teal, see the vignettes:

Author

Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu

Chendi Liao (liaoc10) chendi.liao@roche.com

Examples 

# Example using stream (ADaM) dataset
data <- teal_data() %>%
  eval_code("set.seed(23) # @linksto ADSL") %>%
  within({
    library(nestcolor)
    library(dplyr)
    ADSL <- rADSL
    ADAE <- rADAE
    ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), "UG"))
    ADAE <- mutate(
      ADAE,
      flag1 = ifelse(AETOXGR == 1, 1, 0),
      flag2 = ifelse(AETOXGR == 2, 1, 0),
      flag3 = ifelse(AETOXGR == 3, 1, 0),
      flag1_filt = rep("Y", n())
    )
  })

join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_g_butterfly(
      label = "Butterfly Plot",
      dataname = "ADAE",
      right_var = choices_selected(
        selected = "SEX",
        choices = c("SEX", "ARM", "RACE")
      ),
      left_var = choices_selected(
        selected = "RACE",
        choices = c("SEX", "ARM", "RACE")
      ),
      category_var = choices_selected(
        selected = "AEBODSYS",
        choices = c("AEDECOD", "AEBODSYS")
      ),
      color_by_var = choices_selected(
        selected = "AETOXGR",
        choices = c("AETOXGR", "None")
      ),
      count_by_var = choices_selected(
        selected = "# of patients",
        choices = c("# of patients", "# of AEs")
      ),
      facet_var = choices_selected(
        selected = NULL,
        choices = c("RACE", "SEX", "ARM")
      ),
      sort_by_var = choices_selected(
        selected = "count",
        choices = c("count", "alphabetical")
      ),
      legend_on = TRUE,
      plot_height = c(600, 200, 2000)
    )
  )
)
#> Initializing tm_g_butterfly
if (interactive()) {
  shinyApp(app$ui, app$server)
}