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Line plot

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,
  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),
  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

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.

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 <- goshawk::rADSL
ADLB <- goshawk::rADLB
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
  dplyr::mutate(
    AVISITCD = dplyr::case_when(
      AVISIT == "SCREENING" ~ "SCR",
      AVISIT == "BASELINE" ~ "BL",
      grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
      TRUE ~ as.character(NA)
    ),
    AVISITCDN = dplyr::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 = dplyr::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"]]

app <- teal::init(
  data = teal.data::cdisc_data(
    adsl <- teal.data::cdisc_dataset("ADSL", ADSL, code = "ADSL <- goshawk::rADSL"),
    teal.data::cdisc_dataset("ADLB", ADLB,
      code = "ADLB <- goshawk::rADLB
              var_labels <- lapply(ADLB, function(x) attributes(x)$label)
              ADLB <- ADLB %>%
                dplyr::mutate(AVISITCD = dplyr::case_when(
                    AVISIT == 'SCREENING' ~ 'SCR',
                    AVISIT == 'BASELINE' ~ 'BL',
                    grepl('WEEK', AVISIT) ~
                      paste('W', stringr::str_extract(AVISIT, '(?<=(WEEK ))[0-9]+')),
                    TRUE ~ as.character(NA)),
                  AVISITCDN = dplyr::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 = dplyr::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']]",
      vars = list(ADSL = adsl, arm_mapping = arm_mapping)
    ),
    check = TRUE
  ),
  modules = teal::modules(
    teal.goshawk::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")
    )
  )
)
#> [INFO] 2023-08-14 13:52:03.4233 pid:1122 token:[] teal.goshawk Initializing tm_g_gh_lineplot
if (interactive()) {
  shinyApp(app$ui, app$server)
}