Function to create a density distribution plot. — g_density_distribution

Default plot displays overall density facetted by visit with treatment arms and combined treatment overlaid.

Usage

g_density_distribution_plot(
  label = "Density Distribution Plot",
  data,
  param_var = "PARAMCD",
  param = "CRP",
  xaxis_var = "AVAL",
  trt_group = "ARM",
  unit = "AVALU",
  loq_flag_var = "LOQFL",
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  color_manual = NULL,
  color_comb = "#39ff14",
  comb_line = TRUE,
  facet_var = "AVISITCD",
  hline_arb = character(0),
  hline_arb_color = "red",
  hline_arb_label = "Horizontal line",
  facet_ncol = 2,
  rotate_xlab = FALSE,
  font_size = 12,
  line_size = 2,
  rug_plot = FALSE
)

Arguments

label: text string used to identify plot.
data: ADaM structured analysis laboratory data frame e.g. ADLB.
param_var: name of variable containing biomarker codes e.g. PARAMCD.
param: biomarker to visualize e.g. IGG.
xaxis_var: name of variable containing biomarker results displayed on X-axis e.g. AVAL.
trt_group: name of variable representing treatment group e.g. ARM.
unit: name of variable containing biomarker unit e.g. AVALU.
loq_flag_var: name of variable containing LOQ flag e.g. LOQFL.
xlim: ('numeric vector') optional, a vector of length 2 to specify the minimum and maximum of the x-axis if the default limits are not suitable.
ylim: ('numeric vector') optional, a vector of length 2 to specify the minimum and maximum of the y-axis if the default limits are not suitable.
color_manual: vector of colors applied to treatment values.
color_comb: name or hex value for combined treatment color.
comb_line: display combined treatment line toggle.
facet_var: variable to use for facetting.
hline_arb: ('numeric vector') value identifying intercept for arbitrary horizontal lines.
hline_arb_color: ('character vector') optional, color for the arbitrary horizontal lines.
hline_arb_label: ('character vector') optional, label for the legend to the arbitrary horizontal lines.
facet_ncol: number of facets per row.
rotate_xlab: 45 degree rotation of x-axis label values.
font_size: font size control for title, x-axis label, y-axis label and legend.
line_size: plot line thickness.
rug_plot: should a rug plot be displayed under the density plot. Note this option is most useful if the data only contains a single treatment group.

Author

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

Balazs Toth (tothb2) toth.balazs@gene.com

Examples

# Example using ADaM structure analysis dataset.

library(stringr)

# original ARM value = dose value
arm_mapping <- list(
  "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination"
)
color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")

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",
        trimws(
          substr(
            AVISIT,
            start = 6,
            stop = str_locate(AVISIT, "DAY") - 1
          )
        )
      ),
    TRUE ~ NA_character_
  )) %>%
  mutate(AVISITCDN = case_when(
    AVISITCD == "SCR" ~ -2,
    AVISITCD == "BL" ~ 0,
    grepl("W", AVISITCD) ~ as.numeric(gsub("\\D+", "", AVISITCD)),
    TRUE ~ NA_real_
  )) %>%
  # use ARMCD values to order treatment in visualization legend
  mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
    ifelse(grepl("B", ARMCD), 2,
      ifelse(grepl("A", ARMCD), 3, NA)
    )
  )) %>%
  mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
  mutate(ARM = factor(ARM) %>%
    reorder(TRTORD))
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]

g_density_distribution_plot(
  label = "Density Distribution Plot",
  data = ADLB,
  param_var = "PARAMCD",
  param = c("CRP"),
  xaxis_var = "AVAL",
  unit = "AVALU",
  color_manual = color_manual,
  color_comb = "#39ff14",
  comb_line = FALSE,
  facet_var = "AVISITCD",
  hline_arb = 1.75,
  hline_arb_color = "black",
  hline_arb_label = "Horizontal Line A",
  facet_ncol = 2,
  rotate_xlab = FALSE,
  font_size = 10,
  line_size = .5
)