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Function to create line plot of summary statistics over time.

Source: R/g_lineplot.R
g_lineplot.Rd

Function to create line plot of summary statistics over time.

Usage

g_lineplot(
  label = "Line Plot",
  data,
  biomarker_var = "PARAMCD",
  biomarker_var_label = "PARAM",
  biomarker,
  value_var = "AVAL",
  unit_var = "AVALU",
  loq_flag_var = "LOQFL",
  ylim = c(NA, NA),
  trt_group,
  trt_group_level = NULL,
  shape = NULL,
  shape_type = NULL,
  time,
  time_level = NULL,
  color_manual = NULL,
  line_type = NULL,
  median = FALSE,
  hline_arb = numeric(0),
  hline_arb_color = "red",
  hline_arb_label = "Horizontal line",
  xtick = ggplot2::waiver(),
  xlabel = xtick,
  rotate_xlab = FALSE,
  plot_font_size = 12,
  dodge = 0.4,
  plot_height = 989,
  count_threshold = 0,
  table_font_size = 12,
  display_center_tbl = TRUE
)

Arguments

label

text string to be displayed as plot label.

data

ADaM structured analysis laboratory data frame e.g. ADLB.

biomarker_var

name of variable containing biomarker names.

biomarker_var_label

name of variable containing biomarker labels.

biomarker

biomarker name to be analyzed.

value_var

name of variable containing biomarker results.

unit_var

name of variable containing biomarker result unit.

loq_flag_var

name of variable containing LOQ flag e.g. LOQFL.

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.

trt_group

name of variable representing treatment group.

trt_group_level

vector that can be used to define the factor level of trt_group.

shape

categorical variable whose levels are used to split the plot lines.

shape_type

vector of symbol types.

time

name of variable containing visit names.

time_level

vector that can be used to define the factor level of time. Only use it when x-axis variable is character or factor.

color_manual

vector of colors.

line_type

vector of line types.

median

boolean whether to display median results.

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.

xtick

a vector to define the tick values of time in x-axis. Default value is ggplot2::waiver().

xlabel

vector with same length of xtick to define the label of x-axis tick values. Default value is ggplot2::waiver().

rotate_xlab

boolean whether to rotate x-axis labels.

plot_font_size

control font size for title, x-axis, y-axis and legend font.

dodge

control position dodge.

plot_height

height of produced plot. 989 pixels by default.

count_threshold

integer minimum number observations needed to show the appropriate bar and point on the plot. Default: 0

table_font_size

float controls the font size of the values printed in the table. Default: 12

display_center_tbl

boolean whether to include table of means or medians

Value

ggplot object

Details

Currently, the output plot can display mean and median of input value. For mean, the error bar denotes 95\ quartile.

Author

Balazs Toth (toth.balazs@gene.com)

Wenyi Liu (wenyi.liu@roche.com)

Examples

# Example using ADaM structure analysis dataset.

library(stringr)
library(dplyr)
library(nestcolor)

# original ARM value = dose value
arm_mapping <- list(
  "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination"
)
color_manual <- c("150mg QD" = "thistle", "Placebo" = "orange", "Combination" = "steelblue")
type_manual <- c("150mg QD" = "solid", "Placebo" = "dashed", "Combination" = "dotted")

ADSL <- rADSL %>% filter(!(ARM == "B: Placebo" & AGE < 40))
ADLB <- rADLB
ADLB <- right_join(ADLB, ADSL[, c("STUDYID", "USUBJID")])
#> Joining with `by = join_by(STUDYID, USUBJID)`
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_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCDN",
  color_manual = color_manual,
  line_type = type_manual,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600
)


g_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCD",
  color_manual = NULL,
  line_type = type_manual,
  median = TRUE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c("BL", "W 1", "W 5"),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600
)


g_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCD",
  color_manual = color_manual,
  line_type = type_manual,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c("BL", "W 1", "W 5"),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600,
  count_threshold = 90,
  table_font_size = 15
)


g_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCDN",
  color_manual = color_manual,
  line_type = type_manual,
  median = TRUE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600
)


g_lineplot(
  label = "Line Plot",
  data = subset(ADLB, SEX %in% c("M", "F")),
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = "SEX",
  time = "AVISITCDN",
  color_manual = color_manual,
  line_type = type_manual,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 1500
)


g_lineplot(
  label = "Line Plot",
  data = subset(ADLB, SEX %in% c("M", "F")),
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = "SEX",
  time = "AVISITCDN",
  color_manual = NULL,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 1500
)