Teal Module for Swimlane Plot — tm_g

This is teal module that generates a swimlane plot (bar plot with markers) for ADaM data

Usage

tm_g_swimlane(
  label,
  dataname,
  bar_var,
  bar_color_var = NULL,
  sort_var = NULL,
  marker_pos_var = NULL,
  marker_shape_var = NULL,
  marker_shape_opt = NULL,
  marker_color_var = NULL,
  marker_color_opt = NULL,
  anno_txt_var = NULL,
  vref_line = NULL,
  plot_height = c(1200L, 400L, 5000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  x_label = "Time from First Treatment (Day)"
)

Arguments

label: (character(1))
menu item label of the module in the teal app.
dataname: analysis data used for plotting, needs to be available in the list passed to the data argument of teal::init(). If no markers are to be plotted in the module, "ADSL" should be the input. If markers are to be plotted, data name for the marker data should be the input
bar_var: teal.transform::choices_selected subject-level numeric variable from dataset to plot as the bar length
bar_color_var: teal.transform::choices_selected color by variable (subject-level)
sort_var: choices_selected sort by variable (subject-level)
marker_pos_var: teal.transform::choices_selected variable for marker position from marker data (Note: make sure that marker position has the same relative start day as bar length variable bar_var
marker_shape_var: teal.transform::choices_selected marker shape variable from marker data
marker_shape_opt: aesthetic values to map shape values (named vector to map shape values to each name). If not NULL, please make sure this contains all possible values for marker_shape_var values, otherwise shape will be assigned by ggplot default
marker_color_var: marker color variable from marker data
marker_color_opt: aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible values for marker_color_var values, otherwise color will be assigned by ggplot default
anno_txt_var: character vector with subject-level variable names that are selected as annotation
vref_line: vertical reference lines
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.
x_label: the label of the x axis

Value

the teal::module() object.

Author

Ting Qi (qit3) qit3@gene.com

Examples

# Example using stream (ADaM) dataset
data <- teal_data() |>
  within({
    library(dplyr)
    ADSL <- rADSL %>%
      mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
      filter(STRATA1 == "A" & ARMCD == "ARM A")
    ADRS <- rADRS %>%
      filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>%
      mutate(AVALC = DCSREAS, ADY = EOSDY) %>%
      rbind(rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>%
      arrange(USUBJID)
  })

datanames(data) <- c("ADSL", "ADRS")
join_keys(data) <- default_cdisc_join_keys[datanames(data)]

ADSL <- data[["ADSL"]]
ADRS <- data[["ADRS"]]

app <- init(
  data = data,
  modules = modules(
    tm_g_swimlane(
      label = "Swimlane Plot",
      dataname = "ADRS",
      bar_var = choices_selected(
        selected = "TRTDURD",
        choices = c("TRTDURD", "EOSDY")
      ),
      bar_color_var = choices_selected(
        selected = "EOSSTT",
        choices = c("EOSSTT", "ARM", "ARMCD", "ACTARM", "ACTARMCD", "SEX")
      ),
      sort_var = choices_selected(
        selected = "ACTARMCD",
        choices = c("USUBJID", "SITEID", "ACTARMCD", "TRTDURD")
      ),
      marker_pos_var = choices_selected(
        selected = "ADY",
        choices = c("ADY")
      ),
      marker_shape_var = choices_selected(
        selected = "AVALC",
        c("AVALC", "AVISIT")
      ),
      marker_shape_opt = c("CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "Death" = 8),
      marker_color_var = choices_selected(
        selected = "AVALC",
        choices = c("AVALC", "AVISIT")
      ),
      marker_color_opt = c(
        "CR" = "green", "PR" = "blue", "SD" = "goldenrod",
        "PD" = "red", "Death" = "black"
      ),
      vref_line = c(30, 60),
      anno_txt_var = choices_selected(
        selected = c("ACTARM", "SEX"),
        choices = c(
          "ARM", "ARMCD", "ACTARM", "ACTARMCD", "AGEGR1",
          "SEX", "RACE", "COUNTRY", "DCSREAS", "DCSREASP"
        )
      )
    )
  )
)
#> Initializing tm_g_swimlane
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}