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 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: (choices_selected) subject-level numeric variable from dataset to plot as the bar length
bar_color_var: (choices_selected) color by variable (subject-level)
sort_var: (choices_selected) sort by variable (subject-level)
marker_pos_var: (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: (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
library(dplyr)
library(nestcolor)

ADSL <- osprey::rADSL %>%
  dplyr::mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
  dplyr::filter(STRATA1 == "A" & ARMCD == "ARM A")
ADRS <- osprey::rADRS

ADRS <- ADRS %>%
  dplyr::filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>%
  mutate(AVALC = DCSREAS, ADY = EOSDY) %>%
  base::rbind(ADRS %>% dplyr::filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>%
  arrange(USUBJID)

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL %>%
      dplyr::mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
      dplyr::filter(STRATA1 == 'A' & ARMCD == 'ARM A')"),
    cdisc_dataset("ADRS", ADRS,
      code = "ADRS <- rADRS
              ADRS <- ADRS %>% dplyr::filter(PARAMCD == 'LSTASDI' & DCSREAS == 'Death') %>%
                      mutate(AVALC = DCSREAS, ADY = EOSDY) %>%
              rbind(ADRS %>% dplyr::filter(PARAMCD == 'OVRINV' & AVALC != 'NE')) %>%
              arrange(USUBJID)"
    ),
    check = TRUE
  ),
  modules = modules(
    tm_g_swimlane(
      label = "Swimlane Plot",
      dataname = "ADRS",
      bar_var = teal.transform::choices_selected(
        selected = "TRTDURD",
        choices = c("TRTDURD", "EOSDY")
      ),
      bar_color_var = teal.transform::choices_selected(
        selected = "EOSSTT",
        choices = c("EOSSTT", "ARM", "ARMCD", "ACTARM", "ACTARMCD", "SEX")
      ),
      sort_var = teal.transform::choices_selected(
        selected = "ACTARMCD",
        choices = c("USUBJID", "SITEID", "ACTARMCD", "TRTDURD")
      ),
      marker_pos_var = teal.transform::choices_selected(
        selected = "ADY",
        choices = c("ADY")
      ),
      marker_shape_var = teal.transform::choices_selected(
        selected = "AVALC",
        c("AVALC", "AVISIT")
      ),
      marker_shape_opt = c("CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "Death" = 8),
      marker_color_var = teal.transform::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 = teal.transform::choices_selected(
        selected = c("ACTARM", "SEX"),
        choices = c(
          "ARM", "ARMCD", "ACTARM", "ACTARMCD", "AGEGR1",
          "SEX", "RACE", "COUNTRY", "DCSREAS", "DCSREASP"
        )
      )
    )
  )
)
#> [INFO] 2023-08-14 13:53:50.9369 pid:1120 token:[] teal.osprey Initializing tm_g_swimlane
if (interactive()) {
  shinyApp(app$ui, app$server)
}