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Teal Module for Swimlane Plot

Source: R/tm_g_swimlane.R
tm_g_swimlane.Rd

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)",
  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

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

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.

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

Ting Qi (qit3) qit3@gene.com

Examples 

# Example using stream (ADaM) dataset
data <- teal_data() %>%
  within({
    library(nestcolor)
    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)
  })

join_keys(data) <- default_cdisc_join_keys[names(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
if (interactive()) {
  shinyApp(app$ui, app$server)
}