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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# forester
<!-- badges: start -->
<!-- badges: end -->
The goal of forester is to make it easy for you to create a publication-quality forest plot with as much or as little information displayed on either side as you require.
## Installation
This package is currently early in development, and must be installed from this github repo.
``` r
devtools::install_github("rdboyes/forester")
```
## Example
Suppose we wish to replicate the following figure published in the NEJM [1]:
forester simply requires the left side of the table (in this case, three columns with Subgroups and counts for each of two groups) and vectors which contain the point estimates and confidence intervals.
```{r example}
library(forester)
table <- readxl::read_excel(here::here("inst/extdata/example_figure_data.xlsx"))
# indent the subgroup if there is a number in the placebo column
table$Subgroup <- ifelse(is.na(table$Placebo),
table$Subgroup,
paste0(" ", table$Subgroup))
# remove indent of the first row
table$Subgroup[1] <- "All Patients"
# use forester to create the table with forest plot
forester(left_side_data = table[,1:3],
estimate = table$Estimate,
ci_low = table$`CI low`,
ci_high = table$`CI high`,
display = FALSE,
xlim = c(-100, 25),
file_path = here::here("man/figures/forester_plot.png"))
```
forester handles the alignment of the graph and the table automatically, so figures with fewer rows or columns should work by simply passing a smaller data frame to the function:
```{r}
forester(left_side_data = table[1:12,1:3],
estimate = table$Estimate[1:12],
ci_low = table$`CI low`[1:12],
ci_high = table$`CI high`[1:12],
display = FALSE,
file_path = here::here("man/figures/fewer_rows.png"))
```
```{r}
forester(left_side_data = table[,1],
estimate = table$Estimate,
ci_low = table$`CI low`,
ci_high = table$`CI high`,
display = FALSE,
file_path = here::here("man/figures/fewer_cols.png"))
```
## Additional Fonts
While Courier has a certain appeal, you might want to give your tables a more modern look. However, due to the difficulty of aligning all elements when using them, the use of non-monospaced fonts should be considered experimental at this stage.
```{r}
library(extrafont)
loadfonts(device = "win")
windowsFonts("Fira Sans" = windowsFont("Fira Sans"))
forester(left_side_data = table[,1:3],
estimate = table$Estimate,
ci_low = table$`CI low`,
ci_high = table$`CI high`,
display = FALSE,
file_path = here::here("man/figures/forester_plot_fira.png"),
font_family = "Fira Sans")
```
Adjusting table properties with different fonts will still work:
```{r}
forester(left_side_data = table[1:12,1:3],
estimate = table$Estimate[1:12],
ci_low = table$`CI low`[1:12],
ci_high = table$`CI high`[1:12],
display = FALSE,
font_family = "Fira Sans",
file_path = here::here("man/figures/fewer_rows_fira.png"))
```
```{r}
windowsFonts("Times New Roman" = windowsFont("Times New Roman"))
forester(left_side_data = table[1:12,1:3],
estimate = table$Estimate[1:12],
ci_low = table$`CI low`[1:12],
ci_high = table$`CI high`[1:12],
display = FALSE,
font_family = "Times New Roman",
file_path = here::here("man/figures/fewer_rows_times.png"))
```
## Adding Arrows (Experimental)
```{r}
forester(left_side_data = table[,1:3],
estimate = table$Estimate,
ci_low = table$`CI low`,
ci_high = table$`CI high`,
display = FALSE,
file_path = here::here("man/figures/forester_plot_arrows.png"),
font_family = "Fira Sans",
xlim = c(-100, 25),
xbreaks = c(-100, -75, -50, -25, 0, 25),
arrows = TRUE,
arrow_labels = c("Inclisiran Better", "Placebo Better"))
```
## Adding additional ggplot objects (Experimental)
Custom ggplot objects can be passed to the `forester` function using the parameter `add_plot`. To align the plot with the rows of the table, the vertical center of the bottom row is at y = 0, and each row is one unit tall on the y axis. `add_plot_width` can be set to customize the width of the plot (units are relative to the width of the table).
```{r}
library(ggplot2)
library(tibble)
ex_plot <- ggplot(tibble(x = rep(1:7, each = 15), y = rep(0:14, times = 7)), aes(x = x, y = y)) +
geom_point()
forester(left_side_data = table[1:15,1:3],
estimate = table$Estimate[1:15],
ci_low = table$`CI low`[1:15],
ci_high = table$`CI high`[1:15],
display = FALSE,
font_family = "Times New Roman",
add_plot = ex_plot,
file_path = here::here("man/figures/add_dots.png"))
```
## References
1. Ray, K. K., Wright, R. S., Kallend, D., Koenig, W., Leiter, L. A., Raal, F. J., Bisch, J. A., Richardson, T., Jaros, M., Wijngaard, P. L. J., Kastelein, J. J. P., & ORION-10 and ORION-11 Investigators. (2020). Two Phase 3 Trials of Inclisiran in Patients with Elevated LDL Cholesterol. The New England Journal of Medicine, 382(16), 1507–1519.