Example 9: Forest Plot
The reporter package is able to embed JPEG images into a report. Here is an example using an image saved from the forestploter package. This package creates customizable forest plots. The technique shown here can be used to embed images from any package.
Program
Note the following about this example:
- The forestploter
package creates customizable forest plots.
- The reporter package can embed JPEG images into any output type that accepts images.
library(grid)
library(forestploter)
library(magrittr)
library(sassy)
options("logr.notes" = FALSE,
"logr.autolog" = TRUE)
# Get temp directory
tmp <- tempdir()
# Open log
lf <- log_open(file.path(tmp, "example9.log"))
# Prepare Data ------------------------------------------------------------
sep("Prepare Data")
put("Read example data from forestploter package")
dt <- read.csv(system.file("extdata", "example_data.csv", package = "forestploter"))
put("Keep needed columns")
dt <- dt[,1:6] %>% put()
put("Indent the subgroup if there is a number in the placebo column")
dt$Subgroup <- ifelse(is.na(dt$Placebo),
dt$Subgroup,
paste0(" ", dt$Subgroup)) %>% put()
put("NA to blank or NA will be transformed to character.")
dt$Treatment <- ifelse(is.na(dt$Treatment), "", dt$Treatment)
dt$Placebo <- ifelse(is.na(dt$Placebo), "", dt$Placebo)
dt$se <- (log(dt$hi) - log(dt$est))/1.96
put("Add blank column for the forest plot to display CI.")
dt$` ` <- paste(rep(" ", 20), collapse = " ")
put("Create confidence interval column to display")
dt$`HR (95% CI)` <- ifelse(is.na(dt$se), "",
sprintf("%.2f (%.2f to %.2f)",
dt$est, dt$low, dt$hi))
put("Final data frame")
put(dt)
# Create Plot -------------------------------------------------------------
sep("Create Plot")
put("Assign Forest Properties")
p <- forest(dt[,c(1:3, 8:9)],
est = dt$est,
lower = dt$low,
upper = dt$hi,
sizes = dt$se,
ci_column = 4,
ref_line = 1,
arrow_lab = c("Placebo Better", "Treatment Better"),
xlim = c(0, 4),
ticks_at = c(0.5, 1, 2, 3))
put("Create temp file name")
tmppth <- tempfile(fileext = ".jpg") %>% put()
put("Turn on jpeg device context")
jpeg(tmppth, width = 600, height = 500)
put("Print plot")
plot(p)
put("Turn off device context")
dev.off()
# Create Report -----------------------------------------------------------
sep("Create Report")
put("Create plot object from jpeg file")
plt <- create_plot(tmppth, 5.5, 7.5)
put("Construct report file path")
pth <- file.path(tmp, "example9.rtf")
put("Create report")
rpt <- create_report(pth, output_type = "RTF", font = "Arial") %>%
titles("Figure 3.1.4", "Forest Plot Comparison of Treated vs. Placebo",
"Safety Population", bold = TRUE, blank_row = "none") %>%
add_content(plt) %>%
footnotes("Program: {Sys.path()}",
"Output: {basename(pth)}", blank_row = "none") %>%
page_header("Sponsor: Sassy", "Study: ABC") %>%
page_footer("Date: {Sys.time()}", right = "Page [pg] of [tpg]")
put("Write report")
res <- write_report(rpt)
# Uncomment to Show report
# file.show(res$modified_path)
# Uncomment to View Log
# file.show(lf)
# Clean Up ----------------------------------------------------------------
# Kill image file
file.remove(tmppth)
log_close()Output
Here is an image of the RTF report produced by the above example:
Log
Here is the log produced by the above forest plot example:
=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/Rtmpc54HUz/log/example9.log
Program Path: C:/packages/sassy/vignettes/sassy-forest.Rmd
Working Directory: C:/packages/sassy/
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: grid stats graphics grDevices utils datasets methods base Other
Packages: tidylog_1.0.2 reporter_1.3.8 libr_1.2.6 fmtr_1.5.9 logr_1.3.3
common_1.0.4 sassy_1.0.8 magrittr_2.0.3 forestploter_0.2.1
Log Start Time: 2022-10-08 22:38:59
=========================================================================
=========================================================================
Prepare Data
=========================================================================
Read example data from forestploter package
Keep needed columns
Subgroup Treatment Placebo est
1 All Patients 781 780 1.869694
2 Sex NA NA NA
3 Male 535 548 1.449472
4 Female 246 232 2.275120
5 Age NA NA NA
6 <65 yr 297 333 1.509242
7 >65 yr 484 447 1.468828
8 <75 yr 638 649 1.477608
9 >75 yr 143 131 1.012617
10 Body-mass index NA NA NA
11 <Median 394 385 1.185109
12 >Median 387 394 1.632055
13 Race NA NA NA
14 White 653 685 1.168173
15 Black 110 87 2.022034
16 Other 18 8 2.622501
17 Baseline Statin Treatment NA NA NA
18 Yes 701 692 2.707430
19 No 80 88 1.655263
20 Intensity of statin treatment NA NA NA
21 High 538 546 2.544263
22 Not High 243 234 1.113885
low hi
1 0.13245636 3.606932
2 NA NA
3 0.06834426 2.830600
4 0.50768005 4.042560
5 NA NA
6 0.67029394 2.348190
7 0.45499227 2.482663
8 0.55014273 2.405073
9 0.34370612 1.681528
10 NA NA
11 0.49170973 1.878509
12 0.01765042 3.246461
13 NA NA
14 0.63731627 1.699029
15 0.82239156 3.221677
16 1.18092223 4.064081
17 NA NA
18 1.17973879 4.235121
19 0.29133093 3.019195
20 NA NA
21 0.88528342 4.203243
22 0.03848006 2.189290
Indent the subgroup if there is a number in the placebo column
All Patients
Sex
Male
Female
Age
<65 yr
>65 yr
<75 yr
>75 yr
Body-mass index
<Median
>Median
Race
White
Black
Other
Baseline Statin Treatment
Yes
No
Intensity of statin treatment
High
Not High
NA to blank or NA will be transformed to character.
Add blank column for the forest plot to display CI.
Create confidence interval column to display
Final data frame
Subgroup Treatment Placebo est
1 All Patients 781 780 1.869694
2 Sex NA
3 Male 535 548 1.449472
4 Female 246 232 2.275120
5 Age NA
6 <65 yr 297 333 1.509242
7 >65 yr 484 447 1.468828
8 <75 yr 638 649 1.477608
9 >75 yr 143 131 1.012617
10 Body-mass index NA
11 <Median 394 385 1.185109
12 >Median 387 394 1.632055
13 Race NA
14 White 653 685 1.168173
15 Black 110 87 2.022034
16 Other 18 8 2.622501
17 Baseline Statin Treatment NA
18 Yes 701 692 2.707430
19 No 80 88 1.655263
20 Intensity of statin treatment NA
21 High 538 546 2.544263
22 Not High 243 234 1.113885
low hi se
1 0.13245636 3.606932 0.3352463
2 NA NA NA
3 0.06834426 2.830600 0.3414741
4 0.50768005 4.042560 0.2932884
5 NA NA NA
6 0.67029394 2.348190 0.2255292
7 0.45499227 2.482663 0.2677894
8 0.55014273 2.405073 0.2485489
9 0.34370612 1.681528 0.2587575
10 NA NA NA
11 0.49170973 1.878509 0.2350221
12 0.01765042 3.246461 0.3508801
13 NA NA NA
14 0.63731627 1.699029 0.1911307
15 0.82239156 3.221677 0.2376520
16 1.18092223 4.064081 0.2234995
17 NA NA NA
18 1.17973879 4.235121 0.2282715
19 0.29133093 3.019195 0.3066481
20 NA NA NA
21 0.88528342 4.203243 0.2561302
22 0.03848006 2.189290 0.3447568
HR (95% CI)
1 1.87 (0.13 to 3.61)
2
3 1.45 (0.07 to 2.83)
4 2.28 (0.51 to 4.04)
5
6 1.51 (0.67 to 2.35)
7 1.47 (0.45 to 2.48)
8 1.48 (0.55 to 2.41)
9 1.01 (0.34 to 1.68)
10
11 1.19 (0.49 to 1.88)
12 1.63 (0.02 to 3.25)
13
14 1.17 (0.64 to 1.70)
15 2.02 (0.82 to 3.22)
16 2.62 (1.18 to 4.06)
17
18 2.71 (1.18 to 4.24)
19 1.66 (0.29 to 3.02)
20
21 2.54 (0.89 to 4.20)
22 1.11 (0.04 to 2.19)
=========================================================================
Create Plot
=========================================================================
Assign Forest Properties
Create temp file name
C:\Users\dbosa\AppData\Local\Temp\Rtmpc54HUz\file4ce84b293714.jpg
Turn on jpeg device context
Print plot
Turn off device context
=========================================================================
Create Report
=========================================================================
Create plot object from jpeg file
Construct report file path
Create report
Write report
# A report specification: 1 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\Rtmpc54HUz/example9.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 0.5 bottom 0.5 left 1 right 1
- line size/count: 9/42
- page_header: left=Sponsor: Sassy right=Study: ABC
- title 1: 'Figure 3.1.4'
- title 2: 'Forest Plot Comparison of Treated vs. Placebo'
- title 3: 'Safety Population'
- footnote 1: 'Program: C:/packages/sassy/vignettes/sassy-forest.Rmd'
- footnote 2: 'Output: example9.rtf'
- page_footer: left=Date: 2022-10-08 22:38:59 center= right=Page [pg] of [tpg]
- content:
# A plot specification:
- path: 'C:\Users\dbosa\AppData\Local\Temp\Rtmpc54HUz\file4ce84b293714.jpg'
- height: 5.5
- width: 7.5
=========================================================================
Log End Time: 2022-10-08 22:38:59
Log Elapsed Time: 0 00:00:00
=========================================================================