Scatter Plot Teal Module For Biomarker Analysis
Source:R/tm_g_gh_scatterplot.R
tm_g_gh_scatterplot.Rd
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 frameADLB
.- 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 theshiny::helpText()
elements are useful.
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)$label)
ADLB <- ADLB %>%
mutate(
AVISITCD = case_when(
AVISIT == "SCREENING" ~ "SCR",
AVISIT == "BASELINE" ~ "BL",
grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
TRUE ~ as.character(NA)
),
AVISITCDN = case_when(
AVISITCD == "SCR" ~ -2,
AVISITCD == "BL" ~ 0,
grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
TRUE ~ as.numeric(NA)
),
AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
TRTORD = case_when(
ARMCD == "ARM C" ~ 1,
ARMCD == "ARM B" ~ 2,
ARMCD == "ARM A" ~ 3
),
ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
ARM = factor(ARM) %>% reorder(TRTORD),
ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
ACTARM = factor(ACTARM) %>% reorder(TRTORD)
)
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]
app <- init(
data = data,
modules = modules(
tm_g_gh_scatterplot(
label = "Scatter Plot",
dataname = "ADLB",
param_var = "PARAMCD",
param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "BASE"),
yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
color_manual = c(
"150mg QD" = "#000000",
"Placebo" = "#3498DB",
"Combination" = "#E74C3C"
),
shape_manual = c("N" = 1, "Y" = 2, "NA" = 0),
plot_height = c(500, 200, 2000),
facet_ncol = 2,
trt_facet = FALSE,
reg_line = FALSE,
font_size = c(12, 8, 20),
dot_size = c(1, 1, 12),
reg_text_size = c(3, 3, 10)
)
)
)
#> Warning: `tm_g_gh_scatterplot()` was deprecated in teal.goshawk 0.1.15.
#> ℹ You should use teal.goshawk::tm_g_gh_correlationplot instead of
#> teal.goshawk::tm_g_gh_scatterplot
#> Initializing tm_g_gh_scatterplot
#> Initializing reporter_previewer_module
if (interactive()) {
shinyApp(app$ui, app$server)
}