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Line plot

Source: R/tm_g_gh_lineplot.R
tm_g_gh_lineplot.Rd

This teal module renders the UI and calls the function that creates a line plot.

Usage 

tm_g_gh_lineplot(
  label,
  dataname = "ADLB",
  param_var = lifecycle::deprecated(),
  param = teal.picks::picks(teal.picks::variables("PARAMCD", "PARAMCD"),
    teal.picks::values(selected = "ALT", multiple = FALSE), check_dataset = FALSE),
  param_var_label = "PARAM",
  xaxis_var = teal.picks::variables(dplyr::starts_with("AVISIT"), "AVISITCD"),
  yaxis_var = teal.picks::variables(c("AVAL", "CHG", "PCHG"), "AVAL"),
  xvar_level = NULL,
  filter_var = lifecycle::deprecated(),
  filter_var_choices = lifecycle::deprecated(),
  trt_group = teal.picks::variables(selected = "ARM"),
  trt_group_level = NULL,
  shape_choices = NULL,
  stat = "mean",
  hline_arb = numeric(0),
  hline_arb_color = "red",
  hline_arb_label = "Horizontal line",
  color_manual = c(getOption("ggplot2.discrete.colour"), c("#ff0000", "#008000",
    "#4ca3dd", "#8a2be2"))[1:4],
  xtick = ggplot2::waiver(),
  xlabel = xtick,
  rotate_xlab = FALSE,
  plot_height = c(600, 200, 4000),
  plot_width = NULL,
  plot_font_size = c(12, 8, 20),
  dodge = c(0.4, 0, 1),
  pre_output = NULL,
  post_output = NULL,
  count_threshold = 0,
  table_font_size = c(12, 4, 20),
  dot_size = c(2, 1, 12),
  plot_relative_height_value = 1000,
  transformators = list(),
  decorators = 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 passed to the data argument of teal::init(). E.g. ADaM structured laboratory data frame ADLB.

param_var

[Deprecated] (character(1)) name of variable containing biomarker codes e.g. PARAMCD.

param

(teal.picks::picks() or teal.transform::choices_selected()) biomarker selected.

param_var_label

(character(1)) single name of variable in analysis data that includes parameter labels.

xaxis_var

(teal.picks::variables() or legacy teal.transform::choices_selected()) name of variable containing biomarker results displayed on x-axis e.g. BASE.

yaxis_var

(teal.picks::variables() or legacy teal.transform::choices_selected()) name of variable containing biomarker results displayed on y-axis e.g. AVAL.

xvar_level

(character()) vector that can be used to define the factor level of xvar. Only use it when xaxis_var is of type character or factor.

filter_var

[Deprecated] data constraint variable.

filter_var_choices

[Deprecated] data constraint variable choices.

trt_group

(teal.picks::variables() or legacy teal.transform::choices_selected()) object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

trt_group_level

(named character()) vector that can be used to define factor level of trt_group.

shape_choices

(character(), teal.picks::variables() or legacy teal.transform::choices_selected()) vector or teal.picks::variables() object with names of ADSL variables which can be used to change shape

stat

(character(1)) string of statistics

hline_arb

(numeric) vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

hline_arb_color

(character) a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.

hline_arb_label

(character) a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.

color_manual

(named character, optional) vector of colors applied to treatment values.

xtick

(numeric()) numeric vector to define the tick values of x-axis when x variable is numeric. Default value is waive().

xlabel

(character()) vector with same length of xtick to define the label of x-axis tick values. Default value is waive().

rotate_xlab

(logical(1)) 45 degree rotation of x-axis values.

plot_height

(numeric(3)) controls plot height.

plot_width

(numeric(3), optional) controls plot width.

plot_font_size

(numeric(3)) control font size for title, x-axis, y-axis and legend font.

dodge

(numeric(3)) controls the position dodge of error bar

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.

count_threshold

(numeric(1)) minimum count of observations (as listed in the output table) to plot nodes on the graph

table_font_size

(numeric(3)) controls the font size of values in the table.

dot_size

(numeric(3)) plot dot size.

plot_relative_height_value

(numeric(1)) numeric value between 500 and 5000 for controlling the starting value of the relative plot height slider

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").

decorators

[Experimental] (named list of lists of teal_transform_module) optional, decorator for tables or plots included in the module output reported. The decorators are applied to the respective output objects.

See section "Decorating Module" below for more details.

Value

A teal::module() object that can be used in a teal::init() call.

Decorating Module

This module generates the following objects, which can be modified in place using decorators:

  • plot (ggplot)

A Decorator is applied to the specific output using a named list of teal_transform_module objects. The name of this list corresponds to the name of the output to which the decorator is applied. See code snippet below:

tm_g_gh_lineplot(
   ..., # arguments for module
   decorators = list(
     plot = teal_transform_module(...) # applied only to `plot` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-module-output", package = "teal.goshawk").

To learn more please refer to the vignette vignette("transform-module-output", package = "teal") or the teal::teal_transform_module() documentation.

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

Wenyi Liu

Balazs Toth

Examples 

# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(stringr)
  library(nestcolor)

  # original ARM value = dose value
  .arm_mapping <- list(
    "A: Drug X" = "150mg QD",
    "B: Placebo" = "Placebo",
    "C: Combination" = "Combination"
  )
  ADSL <- teal.data::rADSL
  ADLB <- teal.data::rADLB
  .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
  ADLB <- ADLB %>%
    mutate(
      AVISITCD = case_when(
        AVISIT == "SCREENING" ~ "SCR",
        AVISIT == "BASELINE" ~ "BL",
        grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
        TRUE ~ as.character(NA)
      ),
      AVISITCDN = case_when(
        AVISITCD == "SCR" ~ -2,
        AVISITCD == "BL" ~ 0,
        grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
        TRUE ~ as.numeric(NA)
      ),
      AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
      TRTORD = case_when(
        ARMCD == "ARM C" ~ 1,
        ARMCD == "ARM B" ~ 2,
        ARMCD == "ARM A" ~ 3
      ),
      ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
      ARM = factor(ARM) %>% reorder(TRTORD),
      ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
      ACTARM = factor(ACTARM) %>% reorder(TRTORD)
    )
  attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
  attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
})

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

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_lineplot(
      label = "Line Plot",
      dataname = "ADLB",
      param = picks(
        variables("PARAMCD", "PARAMCD"),
        values(selected = "ALT", multiple = FALSE),
        check_dataset = FALSE
      ),
      shape_choices = c("SEX", "RACE"),
      xaxis_var = variables("AVISITCD", "AVISITCD"),
      yaxis_var = variables(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = variables(c("ARM", "ACTARM"), "ARM"),
      hline_arb = c(20.5, 19.5),
      hline_arb_color = c("red", "green"),
      hline_arb_label = c("A", "B")
    )
  )
)
#> Initializing tm_g_gh_lineplot
#> Warning: rlang::dots_list(..., .ignore_empty = "trailing")
#>  - Setting explicit `selected` while `choices` are delayed (set using `tidyselect`) doesn't guarantee that `selected` is a subset of `choices`.
if (interactive()) {
  shinyApp(app$ui, app$server)
}