Skip to contents

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)

ADSL <- rADSL
ADRS <- 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)

x <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = "ADSL <- rADSL"),
    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 = choices_selected(selected = "TRTDURD", choices = c("TRTDURD", "EOSDY")),
      bar_color_var = choices_selected(
        selected = "EOSSTT",
        choices = c("EOSSTT", "ARM", "ARMCD", "ACTARM", "ACTARMCD", "AGEGR1", "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"
        )
      )
    )
  )
)
#> [INFO] 2022-06-17 09:56:31.6196 pid:1163 token:[] teal.osprey Initializing tm_g_swimlane
if (FALSE) {
shinyApp(x$ui, x$server)
}