Create a Figure
The sassy system of functions also supports reports with graphics. Plots from the popular ggplot2 package can be added to a report. The following example illustrates such a report.
Program
Note the following about this example:
- The plots are created using ggplot2 and the
create_plot()function. - The plots are added to the report with the
add_content()function, just like the tables in the previous examples. - The reporter package allows you to add multiple pieces of content to the same report.
- Titles, footnotes, and other report enhancements are added to the figure just like previous examples.
library(tidyverse)
library(sassy)
# Prepare Log -------------------------------------------------------------
options("logr.autolog" = TRUE,
"logr.notes" = FALSE)
# Get path to temp directory
tmp <- tempdir()
# Get sample data directory
dir <- system.file("extdata", package = "sassy")
# Open log
lgpth <- log_open(file.path(tmp, "example3.log"))
# Load and Prepare Data ---------------------------------------------------
sep("Prepare Data")
# Define data library
libname(sdtm, dir, "csv")
# Loads data into workspace
lib_load(sdtm)
# Prepare data
dm_mod <- sdtm.DM |>
select(USUBJID, SEX, AGE, ARM) |>
filter(ARM != "SCREEN FAILURE") |>
datastep({
if (AGE >= 18 & AGE <= 24)
AGECAT = "18 to 24"
else if (AGE >= 25 & AGE <= 44)
AGECAT = "25 to 44"
else if (AGE >= 45 & AGE <= 64)
AGECAT <- "45 to 64"
else if (AGE >= 65)
AGECAT <- ">= 65"
}) |> put()
put("Get population counts")
arm_pop <- count(dm_mod, ARM) |> put()
sex_pop <- count(dm_mod, SEX) |> put()
agecat_pop <- count(dm_mod, AGECAT) |> put()
# Convert agecat to factor so rows will sort correctly
agecat_pop$AGECAT <- factor(agecat_pop$AGECAT, levels = c("18 to 24",
"25 to 44",
"45 to 64",
">= 65"))
# Sort agecat
agecat_pop <- agecat_pop |> arrange(AGECAT)
# Create Plots ------------------------------------------------------------
plt1 <- ggplot(data = arm_pop, aes(x = ARM, y = n)) +
geom_col(fill = "#0000A0") +
geom_text(aes(label = n), vjust = 1.5, colour = "white") +
labs(x = "Treatment Group", y = "Number of Subjects (n)")
plt2 <- ggplot(data = sex_pop, aes(x = SEX, y = n)) +
geom_col(fill = "#00A000") +
geom_text(aes(label = n), vjust = 1.5, colour = "white") +
labs(x = "Biological Sex", y = "Number of Subjects (n)")
plt3 <- ggplot(data = agecat_pop, aes(x = AGECAT, y = n)) +
geom_col(fill = "#A00000") +
geom_text(aes(label = n), vjust = 1.5, colour = "white") +
labs(x = "Age Categories", y = "Number of Subjects (n)")
# Report ------------------------------------------------------------------
sep("Create and print report")
pth <- file.path(tmp, "output/example3.rtf")
page1 <- create_plot(plt1, 4.5, 7) |>
titles("Figure 1.1", "Distribution of Subjects by Treatment Group",
bold = TRUE, font_size = 11)
page2 <- create_plot(plt2, 4.5, 7) |>
titles("Figure 1.2", "Distribution of Subjects by Biological Sex",
bold = TRUE, font_size = 11)
page3 <- create_plot(plt3, 4.5, 7) |>
titles("Figure 1.2", "Distribution of Subjects by Age Category",
bold = TRUE, font_size = 11)
rpt <- create_report(pth, output_type = "RTF", font = "Arial") |>
set_margins(top = 1, bottom = 1) |>
page_header("Sponsor: Company", "Study: ABC") |>
add_content(page1) |>
add_content(page2) |>
add_content(page3) |>
footnotes("Program: DM_Figure.R") |>
page_footer(paste0("Date Produced: ", fapply(Sys.time(), "%d%b%y %H:%M")),
right = "Page [pg] of [tpg]")
write_report(rpt)
# Clean Up ----------------------------------------------------------------
# Unload library from workspace
lib_unload(sdtm)
# Close log
log_close()
# View files
# file.show(pth)
# file.show(lgpth)Output
Here are the three pages of the report:
Log
Here is the log for the above program:
=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpqUcwY4/log/example3.log
Working Directory: C:/packages/Testing
User Name: dbosa
R Version: 4.0.5 (2021-03-31)
Machine: SOCRATES x86-64
Operating System: Windows 10 x64 build 19041
Log Start Time: 2021-06-27 19:00:45
=========================================================================
=========================================================================
Prepare Data
=========================================================================
# library 'sdtm': 4 items
- attributes: csv not loaded
- path: C:/Users/dbosa/Documents/R/win-library/4.0/sassy/extdata
- items:
Name Extension Rows Cols Size LastModified
1 AE csv 150 27 88.1 Kb 2021-04-04 11:55:58
2 DM csv 87 24 45.2 Kb 2021-04-04 11:55:58
3 SV csv 685 10 69.9 Kb 2021-04-04 11:55:58
4 VS csv 3358 17 467 Kb 2021-04-04 11:55:58
lib_load: library 'sdtm' loaded
select: dropped 20 variables (STUDYID, DOMAIN, SUBJID, RFSTDTC, RFENDTC, …)
filter: removed 2 rows (2%), 85 rows remaining
datastep: columns decreased from 4 to 5
# A tibble: 85 x 5
USUBJID SEX AGE ARM AGECAT
<chr> <chr> <dbl> <chr> <chr>
1 ABC-01-049 M 39 ARM D 25 to 44
2 ABC-01-050 M 47 ARM B 45 to 64
3 ABC-01-051 M 34 ARM A 25 to 44
4 ABC-01-052 F 45 ARM C 45 to 64
5 ABC-01-053 F 26 ARM B 25 to 44
6 ABC-01-054 M 44 ARM D 25 to 44
7 ABC-01-055 F 47 ARM C 45 to 64
8 ABC-01-056 M 31 ARM A 25 to 44
9 ABC-01-113 M 74 ARM D >= 65
10 ABC-01-114 F 72 ARM B >= 65
# ... with 75 more rows
Get population counts
count: now 4 rows and 2 columns, ungrouped
# A tibble: 4 x 2
ARM n
<chr> <int>
1 ARM A 20
2 ARM B 21
3 ARM C 21
4 ARM D 23
count: now 2 rows and 2 columns, ungrouped
# A tibble: 2 x 2
SEX n
<chr> <int>
1 F 32
2 M 53
count: now 4 rows and 2 columns, ungrouped
# A tibble: 4 x 2
AGECAT n
<chr> <int>
1 >= 65 13
2 18 to 24 5
3 25 to 44 23
4 45 to 64 44
=========================================================================
Create and print report
=========================================================================
# A report specification: 3 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpqUcwY4/output/example3.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 1 bottom 1 left 1 right 1
- line size/count: 107/41
- page_header: left=Sponsor: Company right=Study: ABC
- footnote 1: 'Program: DM_Figure.R'
- page_footer: left=Date Produced: 27Jun21 19:00 center= right=Page [pg] of [tpg]
- content:
# A plot specification:
- data: 4 rows, 2 cols
- layers: 2
- height: 4.5
- width: 7
- title 1: 'Figure 1.1'
- title 2: 'Distribution of Subjects by Treatment Group'
# A plot specification:
- data: 2 rows, 2 cols
- layers: 2
- height: 4.5
- width: 7
- title 1: 'Figure 1.2'
- title 2: 'Distribution of Subjects by Biological Sex'
# A plot specification:
- data: 4 rows, 2 cols
- layers: 2
- height: 4.5
- width: 7
- title 1: 'Figure 1.2'
- title 2: 'Distribution of Subjects by Age Category'
lib_sync: synchronized data in library 'sdtm'
lib_unload: library 'sdtm' unloaded
=========================================================================
Log End Time: 2021-06-27 19:00:46
Log Elapsed Time: 0 00:00:00
=========================================================================
Next: Example 4: AE Table