Line plot — tm_g_gh_lineplot • teal.goshawk

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

Usage

tm_g_gh_lineplot(
  label,
  dataname,
  param_var,
  param,
  param_var_label = "PARAM",
  xaxis_var,
  yaxis_var,
  xvar_level = NULL,
  filter_var = yaxis_var,
  filter_var_choices = filter_var,
  trt_group,
  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()
)

Arguments

label: menu item label of the module in the teal app.
dataname: analysis data passed to the data argument of init. E.g. ADaM structured laboratory data frame ADLB.
param_var: name of variable containing biomarker codes e.g. PARAMCD.
param: biomarker selected.
param_var_label: single name of variable in analysis data that includes parameter labels.
xaxis_var: single name of variable in analysis data that is used as x-axis in the plot for the respective goshawk function.
yaxis_var: single name of variable in analysis data that is used as summary variable in the respective goshawk function.
xvar_level: vector that can be used to define the factor level of xvar. Only use it when xvar is character or factor.
filter_var: data constraint variable.
filter_var_choices: data constraint variable choices.
trt_group: choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.
trt_group_level: vector that can be used to define factor level of trt_group.
shape_choices: Vector or choices_selected object with names of ADSL variables which can be used to change shape
stat: string of statistics
hline_arb: numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.
hline_arb_color: a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.
hline_arb_label: a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.
color_manual: string vector representing customized colors
xtick: numeric vector to define the tick values of x-axis when x variable is numeric. Default value is waive().
xlabel: vector with same length of xtick to define the label of x-axis tick values. Default value is waive().
rotate_xlab: logical(1) value indicating whether to rotate x-axis labels.
plot_height: controls plot height.
plot_width: optional, controls plot width.
plot_font_size: control font size for title, x-axis, y-axis and legend font.
dodge: 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: minimum count of observations (as listed in the output table) to plot nodes on the graph
table_font_size: controls the font size of values in the table
dot_size: plot dot size.
plot_relative_height_value: 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").

Value

shiny 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:

vignette("reportable-shiny-application", package = "teal.reporter")
vignette("adding-support-for-reporting-to-custom-modules", package = "teal")

Author

Wenyi Liu (luiw2) wenyi.liu@roche.com

Balazs Toth (tothb2) toth.balazs@gene.com

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"
  )
  set.seed(1) # @linksto ADSL ADLB
  ADSL <- rADSL
  ADLB <- 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_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      shape_choices = c("SEX", "RACE"),
      xaxis_var = choices_selected("AVISITCD", "AVISITCD"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(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
if (interactive()) {
  shinyApp(app$ui, app$server)
}