The shape_plot() and forest_plot()
functions return both a plot and the code used to generate plot (which
will be shown in the RStudio Viewer pane). Examples of generated code
are shown below.
Shape plot
my_results <- data.frame(
x = c( 12, 14, 15.5, 18),
est = c(0.05, 0.21, 0.15, 0.32),
se = c(0.05, 0.05, 0.05, 0.05)
)
shape <- shape_plot(my_results,
xlims = c(10, 20),
ylims = c(0.75, 2),
exponentiate = TRUE,
printplot = FALSE)The code now stored in shape$code and shown in the
RStudio Viewer pane is:
library(ggplot2)
datatoplot <- my_results
# Create the plot with main aesthetics
plot <- ggplot(datatoplot, aes(x = x, y = exp(est))) +
# Plot the point estimates
geom_point(aes(size = 1),
shape = 15,
colour = "black",
fill = "black",
stroke = 0.5) +
# Plot point estimates text
geom_text(aes(y = exp(est+1.96*se),
label = format(round(exp(est), 2), nsmall = 2)),
vjust = -0.8,
size = 3.092846,
colour = "black") +
# Plot the CIs
geom_linerange(aes(ymin = exp(est-1.96*se),
ymax = exp(est+1.96*se)),
linewidth = 0.5) +
# Set the scale for the size of boxes
scale_radius(guide = "none",
limits = c(0, NA_real_),
range = c(0, 3)) +
# Use identity for aesthetic scales
scale_shape_identity() +
scale_colour_identity() +
scale_fill_identity() +
# Set the y-axis scale
scale_y_continuous(trans = "log") +
# Add titles
xlab("Risk factor") +
ylab("Estimate (95% CI)") +
# Plot like a CKB plot
ckbplotr::ckb_style(xlims = c(10, 20),
ylims = c(0.75, 2),
gap = c(0.025, 0.025),
ext = c(0.025, 0.025),
ratio = 1.5,
base_size = 11,
base_line_size = 0.5,
colour = "black") +
# Add theme
theme(legend.position = "top")
Forest plot
my_results <- data.frame(
subgroup = c("men", "women", "35_49", "50_64", "65_79"),
est = c( 0.45, 0.58, 0.09, 0.35, 0.6),
se = c( 0.07, 0.06, 0.06, 0.05, 0.08)
)
forest <- forest_plot(my_results, printplot = FALSE)The code now stored in forest$code and shown in the
RStudio Viewer pane is:
library(ggplot2)
# Prepare data to be plotted using ckbplotr::forest_data()
datatoplot <- ckbplotr::forest_data(panels = my_results,
panel.names = "1",
col.estimate = "est",
col.stderr = "se")
# Create the ggplot
ggplot(datatoplot, aes(y = row, x = estimate_transformed)) +
# Put the different panels in side-by-side plots using facets
facet_wrap(vars(panel), nrow = 1) +
# Add a line at null effect
annotate(geom = "segment",
y = 0.7,
yend = Inf,
x = 1,
xend = 1,
linewidth = 0.5,
colour = "black") +
# Plot points at the transformed estimates
geom_point(data = ~ dplyr::filter(.x,
estimate_transformed > 0.8,
estimate_transformed < 2.2,
!as_diamond),
shape = 15,
size = 3,
colour = "black",
fill = "black",
stroke = 0,
na.rm = TRUE) +
# Plot the CIs
geom_errorbar(aes(xmin = pmin(pmax(lci_transformed, 0.8), 2.2),
xmax = pmin(pmax(uci_transformed, 0.8), 2.2)),
data = ~ dplyr::filter(.x, !is.na(estimate_transformed), !as_diamond),
colour = "black",
width = 0,
linewidth = 0.5,
na.rm = TRUE) +
# Add columns to right side of panels
## column auto_estcolumn
ckbplotr::geom_text_move(aes(y = row,
x = 2.2,
label = `auto_estcolumn`),
move_x = unit(0.9, "mm"),
hjust = 0,
size = 3.092846,
colour = "black",
na.rm = TRUE,
parse = FALSE) +
ckbplotr::geom_text_move(aes(y = - 0,
x = 2.2,
label = title),
move_x = unit(0.9, "mm"),
hjust = 0,
size = 3.092846,
colour = "black",
fontface = "bold",
lineheight = 1,
data = ~ dplyr::tibble(panel = sort(unique(.[["panel"]])),
title = "HR (95% CI)")) +
# Add xlab below each axis
geom_text(aes(y = Inf,
x = 1.32665,,
label = xlab),
hjust = 0.5,
size = 3.092846,
colour = "black",
vjust = 4.4,
fontface = "bold",
data = ~ dplyr::tibble(panel = sort(unique(.[["panel"]])),
xlab = "HR (95% CI)")) +
# Set coordinate system
coord_cartesian(clip = "off",
xlim = c(0.8, 2.2)) +
# Set the scale for the x axis (the estimates and CIs)
scale_x_continuous(trans = "log",
limits = c(0.8, 2.2),
breaks = c(0.5, 1, 1.5, 2, 2.5),
expand = c(0,0)) +
# Set the scale for the y axis (the rows)
scale_y_continuous(trans = "reverse",
breaks = attr(datatoplot, "rowlabels")$row,
labels = attr(datatoplot, "rowlabels")$row.label,
limits = c(max(attr(datatoplot, "rowlabels")$row) + 0.7, NA),
expand = c(0,0)) +
# Control the overall look of the plot
theme(text = element_text(size = 11, colour = "black"),
line = element_line(linewidth = 0.5),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
plot.title = element_blank(),
axis.line.x = element_line(colour = "black", linewidth = 0.5, lineend = "round"),
axis.title = element_blank(),
axis.ticks.x = element_line(colour = "black"),
axis.ticks.length.x = unit(2.75, "pt"),
axis.text.x = element_text(colour = "black",,
margin = margin(t = 4.4),
vjust = 1),
axis.ticks.y = element_blank(),
axis.ticks.length.y = unit(0, "pt"),
axis.line.y = element_blank(),
axis.text.y = ggtext::element_markdown(hjust = 0,
colour = "black",
margin = margin(r = 2.9, unit = "mm")),
panel.border = element_blank(),
panel.spacing = unit(24.5, "mm") + unit(5, "mm") + unit(2.9, "mm"),
strip.background = element_blank(),
strip.placement = "outside",
strip.text = element_blank(),
legend.position = "none",
plot.background = element_blank(),
plot.margin = margin(8, 8, 8, 8, "mm") + unit(c(0, 24.5, 0, 0), "mm"))