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Waterfall Plot

Source: R/g_waterfall.R
g_waterfall.Rd

Waterfall plot is often used in Early Development (ED) to present each individual patient’s best response to a particular drug based on a parameter.

Usage

g_waterfall(
  bar_id,
  bar_height,
  sort_by = NULL,
  col_by = NULL,
  bar_color_opt = NULL,
  anno_txt = NULL,
  href_line = NULL,
  facet_by = NULL,
  show_datavalue = TRUE,
  add_label = NULL,
  gap_point = NULL,
  ytick_at = 20,
  y_label = "Best % Change from Baseline",
  title = "Waterfall Plot"
)

Arguments

bar_id

(vector)
contains IDs to identify each bar

bar_height

numeric vector to be plotted as height of each bar

sort_by

(vector)
used to sort bars, default is NULL in which case bars are ordered by decreasing height

col_by

(vector)
used to color bars, default is NULL in which case bar_id is taken if the argument bar_color_opt is provided

bar_color_opt

(vector)
aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible values for col_by values, otherwise default ggplot color will be assigned, please note that NULL needs to be specified in this case

anno_txt

(dataframe)
contains subject-level variables to be displayed as annotation below the waterfall plot, default is NULL

href_line

(numeric vector)
to plot horizontal reference lines, default is NULL

facet_by

(vector)
to facet plot and annotation table, default is NULL

show_datavalue

(boolean)
controls whether value of bar height is shown, default is TRUE

add_label

(vector)
of one subject-level variable to be added to each bar except for bar_height, default is NULL

gap_point

(numeric)
value for adding bar break when some bars are significantly higher than others, default is NULL

ytick_at

(numeric)
optional bar height axis interval, default is 20

y_label

(string)
label for bar height axis, default is "Best % Change from Baseline"

title

(string)
displayed as plot title, default is "Waterfall Plot"

Value

plot object

Author

Xuefeng Hou (houx14) houx14@gene.com

Ting Qi (qit3) qit3@gene.com

Examples

library(tidyr)
library(dplyr)
library(nestcolor)

g_waterfall(
  bar_id = letters[1:3], bar_height = c(3, 5, -1),
  bar_color_opt = c("red", "green", "blue")
)


# Example 1
ADSL <- osprey::rADSL[1:15, ]
ADRS <- osprey::rADRS %>%
  filter(USUBJID %in% ADSL$USUBJID)
ADTR <- osprey::rADTR %>%
  filter(USUBJID %in% ADSL$USUBJID) %>%
  select(USUBJID, PCHG) %>%
  group_by(USUBJID) %>%
  slice(which.min(PCHG))

TR_SL <- inner_join(ADSL, ADTR, by = "USUBJID", multiple = "all")

SUB_ADRS <- ADRS %>%
  filter(PARAMCD == "BESRSPI" | PARAMCD == "INVET") %>%
  select(USUBJID, PARAMCD, AVALC, AVISIT, ADY) %>%
  spread(PARAMCD, AVALC)

ANL <- TR_SL %>%
  left_join(SUB_ADRS, by = "USUBJID", multiple = "all") %>%
  mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1)

anno_txt_vars <- c("TRTDURD", "BESRSPI", "INVET", "SEX", "BMRKR2")

g_waterfall(
  bar_height = ANL$PCHG,
  bar_id = sub(".*-", "", ANL$USUBJID),
  col_by = ANL$SEX,
  sort_by = ANL$ARM,
  # bar_color_opt = c("F" = "red", "M" = "green", "U" = "blue"),
  anno_txt = ANL[, anno_txt_vars],
  facet_by = NULL,
  href_line = c(-30, 20),
  add_label = ANL$BESRSPI,
  ytick_at = 20,
  gap_point = NULL,
  show_datavalue = TRUE,
  y_label = "Best % Change from Baseline",
  title = "Waterfall Plot"
)


# Example 2 facetting
anno_txt_vars <- c("BESRSPI", "INVET")

g_waterfall(
  bar_id = sub(".*-", "", ANL$USUBJID),
  bar_height = ANL$PCHG,
  sort_by = ANL$COUNTRY,
  col_by = ANL$SEX,
  bar_color_opt = c("F" = "tomato", "M" = "skyblue3", "U" = "darkgreen"),
  anno_txt = ANL[, anno_txt_vars],
  facet_by = ANL$STRATA2,
  href_line = c(-30, 20),
  add_label = ANL$BESRSPI,
  ytick_at = 20,
  gap_point = 260,
  y_label = "Best % Change from Baseline",
  title = "Waterfall Plot"
)


# Example 3 extreme value
ANL$PCHG[3] <- 99
ANL$PCHG[5] <- 199
ANL$PCHG[7] <- 599
ANL$BESRSPI[3] <- "PD"
ANL$BESRSPI[5] <- "PD"
ANL$BESRSPI[7] <- "PD"

g_waterfall(
  bar_id = sub(".*-", "", ANL$USUBJID),
  bar_height = ANL$PCHG,
  sort_by = ANL$ARM,
  col_by = ANL$SEX,
  bar_color_opt = c("F" = "tomato", "M" = "skyblue3", "U" = "darkgreen"),
  anno_txt = ANL[, anno_txt_vars],
  facet_by = NULL,
  href_line = c(-30, 20),
  add_label = ANL$BESRSPI,
  ytick_at = 20,
  gap_point = 260,
  y_label = "Best % Change from Baseline",
  title = "Waterfall Plot"
)