Example 12: Combined Figure

There are a few packages in R that can combine multiple figures into a single image. This image can then be embedded into a report to create a combined figure. Here is an example using the patchwork package.

Program

Note the following about this example:

The patchwork package creates combined plots.
The reporter package can embed patchwork images into any output type that accepts images.

library(tidyverse)
library(sassy)
library(patchwork)


# 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, "example12.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("Convert agecat to factor it will sort correctly")
dm_mod$AGECAT <- factor(dm_mod$AGECAT, levels = c("18 to 24", 
                                                  "25 to 44",
                                                  "45 to 64",
                                                  ">= 65"))

put("Split by ARM")
dm_sub <- split(dm_mod, factor(dm_mod$ARM))
                     

# Create Plots ------------------------------------------------------------

sep("Create Plots")

put("Create plot for ARM A")
plt1 <- ggplot(dm_sub$`ARM A`, aes(x = AGECAT, fill = SEX)) + 
  geom_bar(position = "dodge") + 
  labs(x = "Age Groups", y = "Number of Subjects (n)", title = "Placebo")  

put("Create plot for ARM B")
plt2 <- ggplot(dm_sub$`ARM B`, aes(x = AGECAT, fill = SEX)) + 
  geom_bar(position = "dodge") + 
  labs(x = "Age Groups", y = "Number of Subjects (n)", title = "Drug 50mg")

put("Create plot for ARM C")
plt3 <- ggplot(dm_sub$`ARM C`, aes(x = AGECAT, fill = SEX)) + 
  geom_bar(position = "dodge") + 
  labs(x = "Age Groups", y = "Number of Subjects (n)", title = "Drug 100mg")

put("Create plot for ARM D")
plt4 <- ggplot(dm_sub$`ARM D`, aes(x = AGECAT, fill = SEX)) + 
  geom_bar(position = "dodge") + 
  labs(x = "Age Groups", y = "Number of Subjects (n)", title = "Competitor")


put("Combine 4 plots into 1 using patchwork")
plts <- (plt1 | plt2) / (plt3 | plt4)


# Report ------------------------------------------------------------------


sep("Create and print report")


pth <- file.path(tmp, "output/example12.rtf")


plt <- create_plot(plts, 4.5, 7) %>% 
  titles("Figure 3.2", "Distribution of Subjects by Treatment Group", 
         font_size = 11, bold = TRUE)


rpt <- create_report(pth, output_type = "RTF", font = "Arial") %>% 
  set_margins(top = 1, bottom = 1) %>% 
  page_header("Sponsor: Company", "Study: ABC") %>% 
  add_content(plt) %>% 
  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 to file
res <- write_report(rpt)


# Clean Up ----------------------------------------------------------------

# Unload library from workspace
lib_unload(sdtm)

# Close log
log_close()

# Uncomment to view files
# file.show(pth)
# file.show(lgpth)

Output

Here is an image of the RTF report produced by the above example:

Log

Here is the log produced by the above combined plot example:

=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpqsSwWj/log/example12.log
Program Path: C:/packages/sassy/vignettes/sassy-pfigure.Rmd
Working Directory: C:/packages/sassy/vignettes
User Name: dbosa
R Version: 4.2.1 (2022-06-23 ucrt)
Machine: SOCRATES x86-64
Operating System: Windows 10 x64 build 19044
Base Packages: stats graphics grDevices utils datasets methods base Other
Packages: tidylog_1.0.2 patchwork_1.1.2 reporter_1.3.8 libr_1.2.8 fmtr_1.5.9
logr_1.3.3 common_1.0.5 sassy_1.0.8 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10
purrr_0.3.5 readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2
Log Start Time: 2022-11-28 17:11:15
=========================================================================

=========================================================================
Prepare Data
=========================================================================

# library 'sdtm': 8 items
- attributes: csv not loaded
- path: C:/Users/dbosa/AppData/Local/R/win-library/4.2/sassy/extdata
- items:

lib_load: library 'sdtm' loaded

select: dropped 20 variables (STUDYID, DOMAIN, SUBJID, RFSTDTC, RFENDTC, …)

filter: removed 2 rows (2%), 85 rows remaining

datastep: columns increased from 4 to 5

Convert agecat to factor it will sort correctly

Split by ARM

=========================================================================
Create Plots
=========================================================================

Create plot for ARM A

Create plot for ARM B

Create plot for ARM C

Create plot for ARM D

Combine 4 plots into 1 using patchwork

=========================================================================
Create and print report
=========================================================================

# A report specification: 1 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpqsSwWj/output/example12.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 1 bottom 1 left 1 right 1
- line size/count: 9/36
- page_header: left=Sponsor: Company right=Study: ABC
- footnote 1: 'Program: DM_Figure.R'
- page_footer: left=Date Produced: 28Nov22 17:11 center= right=Page [pg] of [tpg]
- content: 
# A plot specification: 
- height: 4.5
- width: 7
- title 1: 'Figure 3.2'
- title 2: 'Distribution of Subjects by Treatment Group'

# A report specification: 1 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpqsSwWj/output/example12.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 1 bottom 1 left 1 right 1
- line size/count: 9/36
- page_header: left=Sponsor: Company right=Study: ABC
- footnote 1: 'Program: DM_Figure.R'
- page_footer: left=Date Produced: 28Nov22 17:11 center= right=Page [pg] of [tpg]
- content: 
# A plot specification: 
- height: 4.5
- width: 7
- title 1: 'Figure 3.2'
- title 2: 'Distribution of Subjects by Treatment Group'

lib_sync: synchronized data in library 'sdtm'

lib_unload: library 'sdtm' unloaded

lib_unload: library 'sdtm' unloaded

=========================================================================
Log End Time: 2022-11-28 17:11:43
Log Elapsed Time: 0 00:00:27
=========================================================================