# 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(sassy)
    library(ggplot2)
    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")

    put("Define data library")
    libname(sdtm, dir, "csv")

    put("Prepare format")
    agefmt <- value(condition(x >= 18 & x <= 24, "18 to 24"),
                    condition(x >= 25 & x <= 44, "25 to 44"),
                    condition(x >= 45 & x <= 64, "45 to 64"),
                    condition(x >= 65, ">= 65"))

    put("Prepare data")
    datastep(sdtm$DM,
             keep = v(USUBJID, SEX, AGE, ARM, AGECAT),
             where = expression(ARM != "SCREEN FAILURE"),
      {

          AGECAT = fapply(AGE, agefmt)

      }) -> dm_mod

    put("Convert agecat to factor it will sort correctly")
    dm_mod$AGECAT <- factor(dm_mod$AGECAT, levels = levels(agefmt))

    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 ----------------------------------------------------------------

    # 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/RtmpkNnsUE/log/example12.log
    Program Path: C:/packages/Testing/procs/ProcsCombinedFigure.R
    Working Directory: C:/packages/Testing/procs
    User Name: dbosa
    R Version: 4.3.1 (2023-06-16 ucrt)
    Machine: SOCRATES x86-64
    Operating System: Windows 10 x64 build 22621
    Base Packages: stats graphics grDevices utils datasets methods base Other
    Packages: tidylog_1.0.2 ggplot2_3.4.2 patchwork_1.1.3 procs_1.0.3
    reporter_1.4.1 libr_1.2.8 fmtr_1.5.9 logr_1.3.4 common_1.0.8 sassy_1.1.0
    Log Start Time: 2023-09-06 21:06:40.53712
    =========================================================================

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

    Define data library

    # library 'sdtm': 7 items
    - attributes: csv not loaded
    - path: C:/Users/dbosa/AppData/Local/R/win-library/4.3/sassy/extdata
    - items:
      Name Extension Rows Cols     Size        LastModified
    1   AE       csv  150   27  88.5 Kb 2023-08-07 17:51:40
    2   DM       csv   87   24  45.5 Kb 2023-08-07 17:51:40
    3   DS       csv  174    9  34.1 Kb 2023-08-07 17:51:40
    4   EX       csv   84   11  26.4 Kb 2023-08-07 17:51:40
    5   IE       csv    2   14  13.4 Kb 2023-08-07 17:51:40
    6   SV       csv  685   10  70.3 Kb 2023-08-07 17:51:40
    7   VS       csv 3358   17 467.4 Kb 2023-08-07 17:51:40

    Load data into workspace

    lib_load: library 'sdtm' loaded

    Prepare format

    # A user-defined format: 4 conditions
      Name Type        Expression    Label Order
    1  obj    U x >= 18 & x <= 24 18 to 24    NA
    2  obj    U x >= 25 & x <= 44 25 to 44    NA
    3  obj    U x >= 45 & x <= 64 45 to 64    NA
    4  obj    U           x >= 65    >= 65    NA

    Prepare data

    datastep: columns decreased from 24 to 5

    # A tibble: 85 × 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
    # ℹ 75 more rows
    # ℹ Use `print(n = ...)` to see more rows

    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\RtmpkNnsUE/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: 06Sep23 21:06 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

    =========================================================================
    Log End Time: 2023-09-06 21:06:43.938549
    Log Elapsed Time: 0 00:00:03
    =========================================================================

Next: Example 13: Mean Change From Baseline