Density Distribution Plot
tm_g_gh_density_distribution_plot.RdThis teal module renders the UI and calls the functions that create a density distribution plot and an accompanying summary table.
Usage
tm_g_gh_density_distribution_plot(
label,
dataname,
param_var,
param,
xaxis_var,
trt_group,
color_manual = NULL,
color_comb = NULL,
plot_height = c(500, 200, 2000),
plot_width = NULL,
font_size = c(12, 8, 20),
line_size = c(1, 0.25, 3),
hline_arb = numeric(0),
hline_arb_color = "red",
hline_arb_label = "Horizontal line",
facet_ncol = 2L,
comb_line = TRUE,
rotate_xlab = FALSE,
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 teal 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.- trt_group
choices_selectedobject 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.
- color_comb
name or hex value for combined treatment color.
- 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.
- line_size
plot line thickness.
- 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.- facet_ncol
numeric value indicating number of facets per row.
- comb_line
display combined treatment line toggle.
- rotate_xlab
45 degree rotation of x-axis values.
- 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 theshiny::helpText()elements are useful.
Examples
# Example using ADaM structure analysis dataset.
library(dplyr)
library(scda)
# original ARM value = dose value
arm_mapping <- list(
"A: Drug X" = "150mg QD",
"B: Placebo" = "Placebo",
"C: Combination" = "Combination"
)
cached_data <- synthetic_cdisc_data("latest")
ADSL <- cached_data$adsl
ADLB <- cached_data$adlb
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
dplyr::mutate(
AVISITCD = dplyr::case_when(
AVISIT == "SCREENING" ~ "SCR",
AVISIT == "BASELINE" ~ "BL",
grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
TRUE ~ as.character(NA)
),
AVISITCDN = dplyr::case_when(
AVISITCD == "SCR" ~ -2,
AVISITCD == "BL" ~ 0,
grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
TRUE ~ as.numeric(NA)
),
AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
TRTORD = dplyr::case_when(
ARMCD == "ARM C" ~ 1,
ARMCD == "ARM B" ~ 2,
ARMCD == "ARM A" ~ 3
),
ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
ARM = factor(ARM) %>% reorder(TRTORD),
ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
ACTARM = factor(ACTARM) %>% reorder(TRTORD)
)
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
app <- teal::init(
data = cdisc_data(
cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
cdisc_dataset(
"ADLB",
ADLB,
code = "ADLB <- synthetic_cdisc_data(\"latest\")$adlb
var_labels <- lapply(ADLB, function(x) attributes(x)$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(arm_mapping = arm_mapping)
),
check = TRUE
),
modules = modules(
tm_g_gh_density_distribution_plot(
label = "Density Distribution Plot",
dataname = "ADLB",
param_var = "PARAMCD",
param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
xaxis_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"
),
color_comb = "#39ff14",
comb_line = TRUE,
plot_height = c(500, 200, 2000),
font_size = c(12, 8, 20),
line_size = c(1, .25, 3),
hline_arb = c(.02, .05),
hline_arb_color = c("red", "black"),
hline_arb_label = c("Horizontal Line A", "Horizontal Line B")
)
)
)
#> [INFO] 2022-10-19 12:19:43.5220 pid:1931 token:[] teal.goshawk Initializing tm_g_gh_density_distribution_plot
if (FALSE) {
shinyApp(app$ui, app$server)
}