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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
)

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

Value

shiny object

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"
  )

  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
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}