Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh

tm_g_gh_scatterplot is deprecated. Please use tm_g_gh_correlationplot instead.

Usage

tm_g_gh_scatterplot(
  label,
  dataname,
  param_var,
  param,
  xaxis_var,
  yaxis_var,
  trt_group,
  color_manual = NULL,
  shape_manual = NULL,
  facet_ncol = 2,
  trt_facet = FALSE,
  reg_line = FALSE,
  rotate_xlab = FALSE,
  hline = NULL,
  vline = NULL,
  plot_height = c(500, 200, 2000),
  plot_width = NULL,
  font_size = c(12, 8, 20),
  dot_size = c(1, 1, 12),
  reg_text_size = c(3, 3, 10),
  pre_output = NULL,
  post_output = NULL
)

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.
xaxis_var: name of variable containing biomarker results displayed on x-axis e.g. BASE.
yaxis_var: name of variable containing biomarker results displayed on y-axis e.g. AVAL.
trt_group: choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.
color_manual: vector of colors applied to treatment values.
shape_manual: vector of symbols applied to LOQ values.
facet_ncol: numeric value indicating number of facets per row.
trt_facet: facet by treatment group trt_group.
reg_line: include regression line and annotations for slope and coefficient in visualization. Use with facet TRUE.
rotate_xlab: 45 degree rotation of x-axis values.
hline: y-axis value to position of horizontal line.
vline: x-axis value to position a vertical line.
plot_height: controls plot height.
plot_width: optional, controls plot width.
font_size: font size control for title, x-axis label, y-axis label and legend.
dot_size: plot dot size.
reg_text_size: font size control for regression line annotations.
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.

Author

Nick Paszty (npaszty) paszty.nicholas@gene.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)

  # 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_scatterplot(
      label = "Scatter Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "BASE"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "150mg QD" = "#000000",
        "Placebo" = "#3498DB",
        "Combination" = "#E74C3C"
      ),
      shape_manual = c("N" = 1, "Y" = 2, "NA" = 0),
      plot_height = c(500, 200, 2000),
      facet_ncol = 2,
      trt_facet = FALSE,
      reg_line = FALSE,
      font_size = c(12, 8, 20),
      dot_size = c(1, 1, 12),
      reg_text_size = c(3, 3, 10)
    )
  )
)
#> Warning: `tm_g_gh_scatterplot()` was deprecated in teal.goshawk 0.1.15.
#> ℹ You should use teal.goshawk::tm_g_gh_correlationplot instead of
#>   teal.goshawk::tm_g_gh_scatterplot
#> Initializing tm_g_gh_scatterplot
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}