This example produces a waterfall plot to identify patients with the best percentage change from baseline. Waterfall plots are used in many industries.
Program
library(ggplot2)
library(sassy)
options("logr.autolog" = TRUE,
"logr.notes" = FALSE,
"procs.print" = FALSE)
# Get temp location for log and report output
tmp <- tempdir()
# Open log
lf <- log_open(file.path(tmp, "example19.log"))
# Get path to sample data
pkg <- system.file("extdata", package = "sassy")
# Get data
libname(adam, pkg, "RData")
# Prepare data ------------------------------------------------------------
sep("Prepare data")
adrs <- adam$adrs
put("Get unique treatment values")
arm_levels <- proc_sort(adrs, by = TRTA, options = nodupkey ,
keep = TRTA)
put("Convert to vector")
arm_levels <- arm_levels[["TRTA"]]
put("Sort data and convert to factors")
df <- proc_sort(adrs, by = PCHG)
df$USUBJID <- factor(df$USUBJID , levels = df$USUBJID)
df$TRTA <- factor(df$TRTA, levels = arm_levels)
put("Set up named vector for ARM columns")
ARM_COLS <- c("#BC3C29", "#0072B5")
names(ARM_COLS) <- arm_levels
put(ARM_COLS)
# Create plot -------------------------------------------------------------
sep("Create plot")
p <- ggplot(df,
aes(x = USUBJID, y = PCHG, fill = TRTA)) +
# Bars — one per subject, coloured by treatment arm
geom_col(width = 0.8, color = "white", linewidth = 0.15) +
# BOR label at top of each bar
# Positive bars: label above bar (vjust < 0)
# Negative bars: label below bar end (vjust > 1)
geom_text(
aes(label = BOR,
vjust = ifelse(PCHG >= 0, -0.4, 1.3)),
size = 2.0,
family = "serif",
color = "grey20",
fontface = "bold"
) +
# RECIST 1.1 reference lines
# +20%: Progressive Disease threshold
geom_hline(yintercept = 20,
linetype = "dotted", color = "grey40",
linewidth = 0.4) +
# -30%: Partial Response threshold
geom_hline(yintercept = -30,
linetype = "dotted", color = "grey40",
linewidth = 0.4) +
# Zero baseline
geom_hline(yintercept = 0,
color = "black", linewidth = 0.35) +
# Colour scale — named dynamically from arm_levels
scale_fill_manual(
values = ARM_COLS,
name = "Treatment"
) +
# Y-axis — plain numbers, no % symbol
# % indicated in axis title instead
scale_y_continuous(
limits = c(-105, 80),
breaks = seq(-100, 60, 20),
labels = function(x) as.character(x)
) +
# X-axis — USUBJID labels, rotated 90°
scale_x_discrete() +
# Labels
labs(
x = "Subject ID",
y = "Best Change from Baseline (%)"
) +
# Theme — publication-ready
theme_classic(base_size = 11, base_family = "serif") +
theme(
plot.title = element_text(size = 12, face = "bold",
hjust = 0,
margin = margin(b = 3)),
plot.subtitle = element_text(size = 8.5, color = "grey50",
hjust = 0,
margin = margin(b = 10)),
axis.title = element_text(size = 10),
axis.text.y = element_text(size = 9, color = "black"),
axis.text.x = element_text(size = 6.5, color = "black",
angle = 90,
hjust = 1, vjust = 0.5),
axis.line = element_line(linewidth = 0.4),
axis.ticks = element_line(linewidth = 0.3),
panel.grid.major.y = element_line(color = "grey93",
linewidth = 0.25),
panel.grid.major.x = element_blank(),
panel.grid.minor = element_blank(),
legend.position = "right",
legend.background = element_rect(fill = "white",
color = "grey80",
linewidth = 0.25),
legend.text = element_text(size = 9),
legend.title = element_text(size = 9, face = "bold"),
plot.margin = margin(12, 16, 8, 10)
)
# Create Report -----------------------------------------------------------
sep("Create Report")
put("Create output path")
pth <- file.path(tmp, "output/example19.rtf") |> put()
put("Create plot object")
plt <- create_plot(p,
height = 4.5,
width = 8.0) |>
titles(
"Figure 2.1.4: Waterfall Plot - Best Percentage Change from Baseline",
"(Intent to Treat)", bold = TRUE, font_size = 11) |>
footnotes(
"RECIST 1.1 thresholds: PR \u2264 \u221230%; PD \u2265 +20%",
"Bar color indicates treatment arm. Label on bar indicates Best Overall Response (BOR).",
italics = TRUE)
put("Create report")
rpt <- create_report(pth,
output_type = "RTF",
orientation = "landscape",
font = "Arial") |>
set_margins(top = 0.5, bottom = 0.5,
left = 0.75, right = 0.75) |>
page_header("Sponsor: Company", right = "Study: XYX") |>
add_content(plt, align = "center") |>
footnotes("Program: waterfall_plot.R", footer = TRUE) |>
page_footer("Date: {fapply(Sys.Date(), 'date9')}", "Confidential",
"Page [pg] of [tpg]")
put("Write report to file")
res <- write_report(rpt)
# Clean up ----------------------------------------------------------------
log_close()
# Comment in to view report and log
# file.show(res$path)
# file.show(lf)
Log
Here is the log:
=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpK6lTDb/log/example19.log
Program Path: C:/Studies/Validation/Gallery/P19.R
Working Directory: C:/Studies/Validation
User Name: dbosa
R Version: 4.6.1 (2026-06-24 ucrt)
Machine: SOCRATES x86-64
Operating System: Windows 10 x64 build 26200
Base Packages: stats graphics grDevices utils datasets methods base
Other Packages: tidylog_1.1.0 macro_0.1.6 procs_1.1.0 reporter_1.5.0 libr_1.4.2
logr_1.4.1 fmtr_1.7.3 common_1.1.5 sassy_1.3.3 ggplot2_4.0.3
Log Start Time: 2026-11-07 07:19:58.031582
=========================================================================
# library 'adam': 3 items
- attributes: RData not loaded
- path: C:/Users/dbosa/AppData/Local/R/win-library/4.6/sassy/extdata
- items:
Name Extension Rows Cols Size LastModified
1 adaapasi RData 985 44 388.4 Kb 2026-11-07 07:05:14
2 adrs RData 60 4 9.2 Kb 2026-11-07 07:05:14
3 adsl RData 152 56 116.1 Kb 2026-11-07 07:05:14
=========================================================================
Prepare data
=========================================================================
Get unique treatment values
proc_sort: input data set 2 rows and 4 columns
by: TRTA
keep: TRTA
order: a
options: nodupkey
as.character: FALSE
na.sort: last
output data set 2 rows and 1 columns
# A tibble: 2 × 1
TRTA
<chr>
1 Treatment A
2 Treatment B
Convert to vector
Sort data and convert to factors
proc_sort: input data set 60 rows and 4 columns
by: PCHG
keep: USUBJID TRTA BOR PCHG
order: a
as.character: FALSE
na.sort: last
output data set 60 rows and 4 columns
# A tibble: 60 × 4
USUBJID TRTA BOR PCHG
<chr> <chr> <chr> <dbl>
1 001-006 Treatment A CR -98.3
2 002-028 Treatment B CR -97.2
3 002-016 Treatment B CR -96.4
4 001-029 Treatment A CR -96
5 002-004 Treatment B CR -94.3
6 001-018 Treatment A CR -89.2
7 001-011 Treatment A CR -82.4
8 001-020 Treatment A CR -82
9 001-024 Treatment A CR -80.8
10 001-025 Treatment A PR -56.6
# ℹ 50 more rows
# ℹ Use `print(n = ...)` to see more rows
Set up named vector for ARM columns
#BC3C29
#0072B5
=========================================================================
Create plot
=========================================================================
=========================================================================
Create Report
=========================================================================
Create output path
C:\Users\dbosa\AppData\Local\Temp\RtmpK6lTDb/output/example19.rtf
Create plot object
Create report
Write report to file
# A report specification: 1 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpK6lTDb/output/example19.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 0.5 bottom 0.5 left 0.75 right 0.75
- lines per page: 42
- content width: 9.5
- content height: 7.5
- line height: 0.17
- page_header: left=Sponsor: Company right=Study: XYX
- page_footer: left=Date: 07NOV2026 center=Confidential right=Page [pg] of [tpg]
- content:
# A plot specification:
- data: 60 rows, 4 cols
- layers: 5
- height: 4.5
- width: 8
- title 1: 'Figure 2.1.4: Waterfall Plot - Best Percentage Change from Baseline'
- title 2: '(Intent to Treat)'
- footnote 1: 'RECIST 1.1 thresholds: PR ≤ −30%; PD ≥ +20%'
- footnote 2: 'Bar color indicates treatment arm. Label on bar indicates Best Overall Response (BOR).'
=========================================================================
Log End Time: 2026-11-07 07:19:59.42934
Log Elapsed Time: 0 00:00:01
=========================================================================