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forest_plot_final.qmd
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---
title: "forest_plot"
author: "Kasandra Ascuña-Durand / Ariana Cardenas"
format: html
editor: source
---
# STUDY
## Conjunto de datos
```{r}
forest <- readr::read_csv(
"data/processed/forest_study.csv")
```
## Librerías
```{r}
library(tidyverse)
library(ggplot2)
library(forestploter)
library(grid)
```
## Exploración
```{r}
colnames(forest)
```
## Paso 1: Ajustar el df para el forest plot
```{r}
forest$var <- ifelse(is.na(forest$IRR1),
forest$var,
paste0(" ", forest$var))
forest$model_type1 <- replace(as.character(forest$model_type1), is.na(forest$model_type1), "")
forest$pvalue1 <- replace(as.character(forest$pvalue1), is.na(forest$pvalue1), "")
forest$model_type2 <- replace(as.character(forest$model_type2), is.na(forest$model_type2), "")
forest$pvalue2 <- replace(as.character(forest$pvalue2), is.na(forest$pvalue2), "")
forest$AIC1 <- replace(as.character(forest$AIC1), is.na(forest$AIC1), "")
forest$AIC2 <- replace(as.character(forest$AIC2), is.na(forest$AIC2), "")
forest$`Adjusted model` <- paste(rep(" ", 20), collapse = " ")
forest$`Unadjusted model` <- paste(rep(" ", 20), collapse = " ")
# Create a confidence interval column to display
forest$`RR (95% CI)1` <- ifelse(is.na(forest$IRR1), "",
sprintf("%.2f (%.2f, %.2f)",
forest$IRR1, forest$lower1, forest$upper1))
forest$`RR (95% CI)2` <- ifelse(is.na(forest$IRR2), "",
sprintf("%.2f (%.2f, %.2f)",
forest$IRR2, forest$lower2, forest$upper2))
forest <- forest %>%
relocate(`Adjusted model`, .after = `upper1`) %>%
relocate(`RR (95% CI)1`, .after = `Adjusted model`) %>%
relocate(`pvalue2`, .after = `RR (95% CI)2`) %>%
relocate(`AIC2`, .after = `pvalue2`)
head(forest)
#Adjusting the names - skeleton for the forest plot
g <- forest[,c(1, 6:9, 14:17)]
colnames(g) <- c("Centralities",
" ","RR (95% CI)","p-value", "AIC",
" ", "RR (95% CI)","p-value", "AIC")
```
## Graficar el forest plot
```{r fig.align="center", echo = FALSE,fig.height = 9, fig.width = 12}
tm <- forest_theme(core=list(
#fg_params=list(hjust = 1, x = 0.9),
bg_params=list(fill = c("lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white",
"lightgray", "white", "white",
"lightgray", "white", "white"
))),
colhead=list(fg_params=list(hjust=0.5, x=0.5)))
study <- forestploter::forest(g,
est = list(forest$IRR1,
forest$IRR2),
lower = list(forest$lower1,
forest$lower2),
upper = list(forest$upper1,
forest$upper2),
ci_column = c(2, 6),
ref_line = c(1, 1),
xlim = list(c(-1, 5), c(-1, 5)),
theme = tm
)
# Bold grouping text
study <- forestploter::edit_plot(study,
row = c(1, 4, 7, 10, 13, 16, 19, 22, 24, 27),
gp = grid::gpar(fontface = "bold"))
# Insert text at the top
study <- insert_text(study,
text = "Adjusted model",
col = 2:4,
part = "header",
gp = grid::gpar(fontface = "bold"))
study <- add_text(study,
text = "Unadjusted model",
col = 5:7,
row = 1,
part = "header",
gp = grid::gpar(fontface = "bold"))
# Add underline at the bottom of the header
study <- add_border(study, part = "header", row = 1, where = "top")
study <- add_border(study, part = "header", row = 2, where = "bottom")
study <- add_border(study, part = "header", row = 1, col = 2:5,
gp = gpar(lwd = 2))
study <- add_border(study, part = "header", row = 1, col = 6:9,
gp = gpar(lwd = 2))
plot(study)
```
```{r}
#ggsave("figures/forest_plot/study.png", study, height = 9, width = 12, dpi = 300)
```
# Work
## Conjunto de datos
```{r}
forest_1 <- readr::read_csv(
"data/processed/forest_work.csv")
```
## Exploración
```{r}
colnames(forest_1)
```
## Paso 1: Ajustar el df para el forest plot
```{r}
forest_1$var <- ifelse(is.na(forest_1$IRR1),
forest_1$var,
paste0(" ", forest_1$var))
forest_1$model_type1 <- replace(as.character(forest_1$model_type1), is.na(forest_1$model_type1), "")
forest_1$pvalue1 <- replace(as.character(forest_1$pvalue1), is.na(forest_1$pvalue1), "")
forest_1$model_type2 <- replace(as.character(forest_1$model_type2), is.na(forest_1$model_type2), "")
forest_1$pvalue2 <- replace(as.character(forest_1$pvalue2), is.na(forest_1$pvalue2), "")
forest_1$AIC1 <- replace(as.character(forest_1$AIC1), is.na(forest_1$AIC1), "")
forest_1$AIC2 <- replace(as.character(forest_1$AIC2), is.na(forest_1$AIC2), "")
forest_1$`Adjusted model` <- paste(rep(" ", 20), collapse = " ")
forest_1$`Unadjusted model` <- paste(rep(" ", 20), collapse = " ")
# Create a confidence interval column to display
forest_1$`RR (95% CI)1` <- ifelse(is.na(forest_1$IRR1), "",
sprintf("%.2f (%.2f, %.2f)",
forest_1$IRR1, forest_1$lower1, forest_1$upper1))
forest_1$`RR (95% CI)2` <- ifelse(is.na(forest_1$IRR2), "",
sprintf("%.2f (%.2f, %.2f)",
forest_1$IRR2, forest_1$lower2, forest_1$upper2))
forest_1 <- forest_1 %>%
relocate(`Adjusted model`, .after = `upper1`) %>%
relocate(`RR (95% CI)1`, .after = `Adjusted model`) %>%
relocate(`pvalue2`, .after = `RR (95% CI)2`) %>%
relocate(`AIC2`, .after = `pvalue2`)
head(forest_1)
g1 <- forest_1[,c(1, 6:9, 14:17)]
colnames(g1) <- c("Centralities",
" ","RR (95% CI)","p-value", "AIC"," ",
"RR (95% CI)","p-value", "AIC")
```
## Graficar el forest plot
```{r fig.align="center", echo = FALSE,fig.height = 9, fig.width = 12}
tm1 <- forest_theme(core=list(
#fg_params=list(hjust = 1, x = 0.9),
bg_params=list(fill = c("lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white"
))),
colhead=list(fg_params=list(hjust=0.5, x=0.5)))
work <- forestploter::forest(g1,
est = list(forest_1$IRR1,
forest_1$IRR2),
lower = list(forest_1$lower1,
forest_1$lower2),
upper = list(forest_1$upper1,
forest_1$upper2),
ci_column = c(2, 6),
ref_line = c(1, 1),
xlim = list(c(-1, 5), c(-1, 5)),
theme = tm1
# ticks_at = list(c(0.1, 0.5, 1, 2.5), c(-1, 0, 2)),
# xlab = c("OR", "Beta"),
)
# Bold grouping text
work <- forestploter::edit_plot(work,
row = c(1, 4, 7, 10, 13, 16, 19, 22, 24, 27),
gp = grid::gpar(fontface = "bold"))
# Insert text at the top
work <- insert_text(work,
text = "Adjusted model",
col = 2:4,
part = "header",
gp = grid::gpar(fontface = "bold"))
work <- add_text(work,
text = "Unadjusted model",
col = 5:7,
row = 1,
part = "header",
gp = grid::gpar(fontface = "bold"))
# Add underline at the bottom of the header
work <- add_border(work, part = "header", row = 1, where = "top")
work <- add_border(work, part = "header", row = 2, where = "bottom")
work <- add_border(work, part = "header", row = 1, col = 2:5,
gp = gpar(lwd = 2))
work <- add_border(work, part = "header", row = 1, col = 6:9,
gp = gpar(lwd = 2))
plot(work)
```
```{r}
#ggsave("figures/forest_plot/work.png", work, height = 9, width = 12, dpi = 300)
```
# Total
## Conjunto de datos
```{r}
forest_2 <- readr::read_csv(
"data/processed/forest_total.csv")
```
## Exploración
```{r}
colnames(forest_2)
```
## Paso 1: Ajustar el df para el forest plot
```{r}
forest_2$var <- ifelse(is.na(forest_2$IRR1),
forest_2$var,
paste0(" ", forest_2$var))
forest_2$model_type1 <- replace(as.character(forest_2$model_type1), is.na(forest_2$model_type1), "")
forest_2$pvalue1 <- replace(as.character(forest_2$pvalue1), is.na(forest_2$pvalue1), "")
forest_2$model_type2 <- replace(as.character(forest_2$model_type2), is.na(forest_2$model_type2), "")
forest_2$pvalue2 <- replace(as.character(forest_2$pvalue2), is.na(forest_2$pvalue2), "")
forest_2$AIC1 <- replace(as.character(forest_2$AIC1), is.na(forest_2$AIC1), "")
forest_2$AIC2 <- replace(as.character(forest_2$AIC2), is.na(forest_2$AIC2), "")
forest_2$`Adjusted model` <- paste(rep(" ", 20), collapse = " ")
forest_2$`Unadjusted model` <- paste(rep(" ", 20), collapse = " ")
# Create a confidence interval column to display
forest_2$`RR (95% CI)1` <- ifelse(is.na(forest_2$IRR1), "",
sprintf("%.2f (%.2f, %.2f)",
forest_2$IRR1, forest_2$lower1, forest_2$upper1))
forest_2$`RR (95% CI)2` <- ifelse(is.na(forest_2$IRR2), "",
sprintf("%.2f (%.2f, %.2f)",
forest_2$IRR2, forest_2$lower2, forest_2$upper2))
forest_2 <- forest_2 %>%
relocate(`Adjusted model`, .after = `upper1`) %>%
relocate(`RR (95% CI)1`, .after = `Adjusted model`) %>%
relocate(`pvalue2`, .after = `RR (95% CI)2`) %>%
relocate(`AIC2`, .after = `pvalue2`)
head(forest_2)
g2 <- forest_2[,c(1, 6:9, 14:17)]
colnames(g2) <- c("Centralities",
" ","RR (95% CI)","p-value", "AIC"," ",
"RR (95% CI)","p-value", "AIC")
```
## Graficar el forest plot
```{r fig.align="center", echo = FALSE,fig.height = 9, fig.width = 12}
tm2 <- forest_theme(core=list(
#fg_params=list(hjust = 1, x = 0.9),
bg_params=list(fill = c("lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white",
"lightgray", "white", "white"
))),
colhead=list(fg_params=list(hjust=0.5, x=0.5)))
total <- forestploter::forest(g2,
est = list(forest_2$IRR1,
forest_2$IRR2),
lower = list(forest_2$lower1,
forest_2$lower2),
upper = list(forest_2$upper1,
forest_2$upper2),
ci_column = c(2, 6),
ref_line = c(1, 1),
xlim = list(c(-1, 5), c(-1, 5)),
theme = tm2
# ticks_at = list(c(0.1, 0.5, 1, 2.5), c(-1, 0, 2)),
# xlab = c("OR", "Beta"),
)
# Bold grouping text
total <- forestploter::edit_plot(total,
row = c(1, 4, 7, 10, 12, 15, 18, 21, 24, 27),
gp = grid::gpar(fontface = "bold"))
# Insert text at the top
total <- insert_text(total,
text = "Adjusted model",
col = 2:4,
part = "header",
gp = grid::gpar(fontface = "bold"))
total <- add_text(total,
text = "Unadjusted model",
col = 5:7,
row = 1,
part = "header",
gp = grid::gpar(fontface = "bold"))
# Add underline at the bottom of the header
total <- add_border(total, part = "header", row = 1, where = "top")
total <- add_border(total, part = "header", row = 2, where = "bottom")
total <- add_border(total, part = "header", row = 1, col = 2:5,
gp = gpar(lwd = 2))
total <- add_border(total, part = "header", row = 1, col = 6:9,
gp = gpar(lwd = 2))
plot(total)
```
```{r}
ggsave("figures/forest_plot/total.png", total, height = 9, width = 12, dpi = 300)
```
```{r}
library(cowplot)
```
```{r fig.align="center", echo = FALSE,fig.height = 9, fig.width = 30}
combined_fplot <- plot_grid(study, work, total, ncol = 3)
combined_fplot
```
```{r}
#ggsave("figures/forest_plot/combined_forest.png", combined_fplot, height = 10, width = 35, dpi = 300)
```