Create a Figure with a By-Group
The sassy system gives you capabilities that few other R packages can match. The system not only support reports with by-groups. You can even apply a by-group to a figure.
Program
Note the following about this example:
- The plot is created as a single plot with no by-groups
- The plot is added to the report with the
add_content()function, just like the figures in the previous example. - The
page_by()function on thecreate_report()statement generates the paging for both the report and plot.
library(tidyverse)
library(sassy)
options("logr.autolog" = TRUE,
"logr.notes" = FALSE)
# Get path to temp directory
tmp <- tempdir()
# Get path to sample data
pkg <- system.file("extdata", package = "sassy")
# Open log
lgpth <- log_open(file.path(tmp, "example3.log"))
sep("Prepare Data")
# Create libname for csv data
libname(sdtm, pkg, "csv")
# Load data into workspace
lib_load(sdtm)
put("Perform joins and basic filters")
prep <- sdtm.DM |>
left_join(sdtm.VS, by = c("USUBJID" = "USUBJID")) |>
select(USUBJID, ARMCD, ARM, VSTESTCD, VSTEST, VSORRES, VISITNUM, VISIT) |>
filter(VSTESTCD %in% c("SYSBP", "DIABP", "PULSE", "TEMP", "RESP"),
ARMCD != "SCRNFAIL") |> put()
put("Group and summarize")
final <- prep |>
group_by(ARMCD, ARM, VSTESTCD, VSTEST, VISITNUM, VISIT) |>
summarize(MEAN = mean(VSORRES, na.rm = TRUE)) |>
filter(VISITNUM > 0 & VISITNUM < 20) |>
mutate(VISIT = factor(VISIT, levels = c("DAY 1", "WEEK 2", "WEEK 4",
"WEEK 6","WEEK 8", "WEEK 12",
"WEEK 16"))) |>
ungroup() |> put()
sep("Create plots and print report")
# Create plot
p <- final |>
ggplot(mapping = aes(y = MEAN, x = VISIT , group = ARM)) +
geom_point(aes(shape = ARM, color = ARM)) +
geom_line(aes(linetype = ARM, color = ARM)) +
scale_x_discrete(name = "Visit") +
scale_y_continuous(name = "Value")
# Construct output path
pth <- file.path(tmp, "output/f_vs.rtf")
# Define report object
rpt <- create_report(pth, output_type = "RTF", font = "Arial") |>
set_margins(top = 1, bottom = 1) |>
page_header("Sponsor: Company", "Study: ABC") |>
page_by(VSTEST, "Vital Sign: ", blank_row = "none") |>
titles("Figure 1.0", "Vital Signs Change from Baseline",
"Safety Population", bold = TRUE) |>
add_content(create_plot(p, 4.5, 9)) |>
footnotes("R Program: VS_Figure.R") |>
page_footer(paste0("Date Produced: ", fapply(Sys.time(), "%d%b%y %H:%M")),
right = "Page [pg] of [tpg]")
# Write report to file system
write_report(rpt)
# Close libname
lib_close(sdtm)
# Close log
log_close()
# View report
# file.show(pth)
# View log
# file.show(lgpth)Output
And here are the first three pages of the report:
Log
Here is the log for the above program:
=========================================================================
Log Path: C:/Users/User/AppData/Local/Temp/Rtmpum5T6o/log/example3.log
Working Directory: C:/packages/Testing
User Name: User
R Version: 4.0.3 (2020-10-10)
Machine: DESKTOP-1F27OR8 x86-64
Operating System: Windows 10 x64 build 18363
Log Start Time: 2021-01-05 08:23:30
=========================================================================
=========================================================================
Prepare Data
=========================================================================
# library 'sdtm': 8 items
- attributes: csv not loaded
- path: C:/Users/User/Documents/R/win-library/4.0/sassy/extdata
- items:
Name Extension Rows Cols Size LastModified
1 AE csv 150 27 88.1 Kb 2020-12-27 23:21:55
2 DA csv 3587 18 527.8 Kb 2020-12-27 23:21:55
3 DM csv 87 24 45.2 Kb 2020-12-27 23:21:55
4 DS csv 174 9 33.7 Kb 2020-12-27 23:21:55
5 EX csv 84 11 26 Kb 2020-12-27 23:21:55
6 IE csv 2 14 13 Kb 2020-12-27 23:21:55
7 SV csv 685 10 69.9 Kb 2020-12-27 23:21:55
8 VS csv 3358 17 467 Kb 2020-12-27 23:21:55
lib_load: library 'sdtm' loaded
Perform joins and basic filters
left_join: added 18 columns (STUDYID.x, DOMAIN.x, STUDYID.y, DOMAIN.y, VSSEQ, …)
> rows only in x 0
> rows only in y ( 0)
> matched rows 3,358 (includes duplicates)
> =======
> rows total 3,358
select: dropped 32 variables (STUDYID.x, DOMAIN.x, SUBJID, RFSTDTC, RFENDTC, …)
filter: removed 246 rows (7%), 3,112 rows remaining
# A tibble: 3,112 x 8
USUBJID ARMCD ARM VSTESTCD VSTEST VSORRES VISITNUM VISIT
<chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr>
1 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 78 0 SCREENING
2 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 76 1 DAY 1
3 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 66 2 WEEK 2
4 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 84 4 WEEK 4
5 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 68 6 WEEK 6
6 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 80 8 WEEK 8
7 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 70 12 WEEK 12
8 ABC-01-049 4 ARM D DIABP Diastolic Blood Pressure 70 16 WEEK 16
9 ABC-01-049 4 ARM D PULSE Pulse Rate 92 0 SCREENING
10 ABC-01-049 4 ARM D PULSE Pulse Rate 84 1 DAY 1
# ... with 3,102 more rows
Group and summarize
group_by: 6 grouping variables (ARMCD, ARM, VSTESTCD, VSTEST, VISITNUM, …)
summarize: now 175 rows and 7 columns, 5 group variables remaining (ARMCD, ARM, VSTESTCD, VSTEST, VISITNUM)
filter (grouped): removed 35 rows (20%), 140 rows remaining
mutate (grouped): converted 'VISIT' from character to factor (0 new NA)
ungroup: no grouping variables
# A tibble: 140 x 7
ARMCD ARM VSTESTCD VSTEST VISITNUM VISIT MEAN
<chr> <chr> <chr> <chr> <dbl> <fct> <dbl>
1 1 ARM A DIABP Diastolic Blood Pressure 1 DAY 1 76.5
2 1 ARM A DIABP Diastolic Blood Pressure 2 WEEK 2 77.6
3 1 ARM A DIABP Diastolic Blood Pressure 4 WEEK 4 78.7
4 1 ARM A DIABP Diastolic Blood Pressure 6 WEEK 6 74.4
5 1 ARM A DIABP Diastolic Blood Pressure 8 WEEK 8 77.1
6 1 ARM A DIABP Diastolic Blood Pressure 12 WEEK 12 78.4
7 1 ARM A DIABP Diastolic Blood Pressure 16 WEEK 16 77.3
8 1 ARM A PULSE Pulse Rate 1 DAY 1 72.6
9 1 ARM A PULSE Pulse Rate 2 WEEK 2 73.4
10 1 ARM A PULSE Pulse Rate 4 WEEK 4 75.8
# ... with 130 more rows
=========================================================================
Create plots and print report
=========================================================================
# A report specification: 5 pages
- file_path: 'C:\Users\User\AppData\Local\Temp\Rtmpum5T6o/output/f_vs.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- line size/count: 108/41
- page by: VSTEST
- page_header: left=Sponsor: Company right=Study: ABC
- title 1: 'Figure 1.0'
- title 2: 'Vital Signs Change from Baseline'
- title 3: 'Safety Population'
- footnote 1: 'R Program: VS_Figure.R'
- page_footer: left=Date Produced: 05Jan21 08:23 center= right=Page [pg] of [tpg]
- content:
# A plot specification:
- data: 140 rows, 7 cols
- layers: 2
- height: 4.5
- width: 9
=========================================================================
Log End Time: 2021-01-05 08:23:50
Log Elapsed Time: 0 00:00:19
=========================================================================
Next: Example 7