Package 'forestploter' reference manual

Title:	Create a Flexible Forest Plot
Description:	Create a forest plot based on the layout of the data. Confidence intervals in multiple columns by groups can be done easily. Editing the plot, inserting/adding text, applying a theme to the plot, and much more.
Authors:	Alimu Dayimu [aut, cre]
Maintainer:	Alimu Dayimu <[email protected]>
License:	MIT + file LICENSE
Version:	1.1.3
Built:	2024-11-08 05:29:33 UTC
Source:	https://github.com/adayim/forestploter

This function can be used to add text to forest plot. The text can be span to multiple rows and columns. The height of the row will be changed accordingly if the text is added to only one row. The width of the text may exceeds the columns provided if the text is too long.

Usage

add_text(
  plot,
  text,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  just = c("center", "left", "right"),
  gp = gpar(),
  padding = unit(1, "mm"),
  parse = FALSE
)
add_text(
  plot,
  text,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  just = c("center", "left", "right"),
  gp = gpar(),
  padding = unit(1, "mm"),
  parse = FALSE
)

Arguments

`plot`	A forest plot object.
`text`	A character or expression vector, see `textGrob`.
`row`	Row to add the text, this will be ignored if the `part` is "header".
`col`	A numeric value or vector indicating the columns the text will be added. The text will span over the column if a vector is given.
`part`	Part to add text, body (default) or header.
`just`	The justification of the text, `"center"` (default), `"left"` or `"right"`.
`gp`	An object of class `"gpar"`, this is the graphical parameter settings of the text. See `gpar`.
`padding`	Padding of the text, default is `unit(1, "mm")`
`parse`	Logical, behaviour for parsing text as plotmath, see `plotmath`

Value

A gtable object.

Edit forest plot

Description

This function is used to edit the graphical parameter of text and background of the forest plot.

Usage

edit_plot(
  plot,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  which = c("text", "background", "ci"),
  gp = gpar(),
  ...
)
edit_plot(
  plot,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  which = c("text", "background", "ci"),
  gp = gpar(),
  ...
)

Arguments

`plot`	A forest plot object.
`row`	A numeric value or vector indicating row number to edit in the dataset. Will edit the whole row if left blank for the body. This will be ignored if the `part` is "header".
`col`	A numeric value or vector indicating column to edit in the dataset. Will edit the whole column if left blank.
`part`	Part to edit, `"body"` (default) or `"header"`.
`which`	Which element to edit, `"text"`, `"background"` or `"ci"` (confidence interval). This will not edit diamond shaped summary CI, please change it with `forest_theme`. Also, change in `ci` will not have any impact on the legend.
`gp`	Pass `gpar` parameters, see `gpar`. It should be passed as `gpar(col = "red")`. For `which = "ci"`, please refer to `forest_theme` `ci_*` parameters for the editable elements.
`...`	Other parameters to be passed to the grobs. For the `"text"`, please see `textGrob` for details and `rectGrob` for `"background"`. This will be ignored if `which = "ci"` as changing parameters for the confidence interval are not allowed except for the graphical parameters.

Value

A gtable object.

Forest plot

Description

A data frame will be used for the basic layout of the forest plot. Graphical parameters can be set using the forest_theme function.

Usage

forest(
  data,
  est,
  lower,
  upper,
  sizes = 0.4,
  ref_line = ifelse(x_trans %in% c("log", "log2", "log10"), 1, 0),
  vert_line = NULL,
  ci_column,
  is_summary = NULL,
  xlim = NULL,
  ticks_at = NULL,
  ticks_digits = NULL,
  ticks_minor = NULL,
  arrow_lab = NULL,
  x_trans = "none",
  xlab = NULL,
  footnote = NULL,
  title = NULL,
  nudge_y = 0,
  fn_ci = makeci,
  fn_summary = make_summary,
  index_args = NULL,
  theme = NULL,
  ...
)
forest(
  data,
  est,
  lower,
  upper,
  sizes = 0.4,
  ref_line = ifelse(x_trans %in% c("log", "log2", "log10"), 1, 0),
  vert_line = NULL,
  ci_column,
  is_summary = NULL,
  xlim = NULL,
  ticks_at = NULL,
  ticks_digits = NULL,
  ticks_minor = NULL,
  arrow_lab = NULL,
  x_trans = "none",
  xlab = NULL,
  footnote = NULL,
  title = NULL,
  nudge_y = 0,
  fn_ci = makeci,
  fn_summary = make_summary,
  index_args = NULL,
  theme = NULL,
  ...
)

Arguments

`data`	Data to be displayed in the forest plot
`est`	Point estimation. Can be a list for multiple columns and/or multiple groups. If the length of the list is larger than then length of `ci_column`, then the values reused for each column and considered as different groups.
`lower`	Lower bound of the confidence interval, same as `est`.
`upper`	Upper bound of the confidence interval, same as `est`.
`sizes`	Size of the point estimation box, can be a unit, vector or a list. Values will be used as it is, no transformation will be applied.
`ref_line`	X-axis coordinates of zero line, default is 1. Provide an atomic vector if different reference line for each `ci_column` is desired.
`vert_line`	Numerical vector, add additional vertical line at given value. Provide a list of numerical vector element if different vertical line for each `ci_column` is desired.
`ci_column`	Column number of the data the CI will be displayed.
`is_summary`	A logical vector indicating if the value is a summary value, which will have a diamond shape for the estimate. Can not be used with multiple group `forestplot`.
`xlim`	Limits for the x axis as a vector of length 2, i.e. c(low, high). It will take the minimum and maximum of the lower and upper value if not provided. This will apply to all CI columns if provided, and will be calculated automatically for each column if not provided. This should be a list with the same length of `ci_column` if different `xlim` for different column is desired.
`ticks_at`	Set X-axis tick-marks point. This will apply to all CI columns if provided, and will be calculated automatically for each column if not provided. This should be a list if different `ticks_at` for different column is desired. Although many efforts have been made to automatically get a pretty ticks break, it will not give a perfect solution, especially if `'log2'` and `'log10'` defined for `x_trans`. Please provide this value if possible.
`ticks_digits`	Number of digits for the x-axis, default is `NULL` to calculate an integer based on `ticks_at` if provided or `lower` and `upper` if not. This should be a numerical vector if different rounding will be applied to different column. If an integer is specified, for example `1L`, trailing zeros after the decimal mark will be dropped. Specify numeric, for example `1`, to keep the trailing zero after the decimal mark.
`ticks_minor`	A numeric vector of positions to draw ticks without labels (optional). The values provided here can be superset or disjoint sets of `ticks_at`.
`arrow_lab`	Labels for the arrows, string vector of length two (left and right). The theme of arrow will inherit from the x-axis. This should be a list if different arrow labels for each column is desired.
`x_trans`	Change axis scale, Allowed values are one of c("none", "log", "log2", "log10"). Default is `"none"`, no transformation will be applied. The formatted label will be used for `scale = "log2"` or `"log10"`, change this in `x_trans`. Set this to `"log"` if x-axis tick marks assume values are exponential, e.g. for logistic regression (OR), survival estimates (HR), Poisson regression etc.
`xlab`	X-axis labels, it will be put under the x-axis. An atomic vector should be provided if different `xlab` for different column is desired.
`footnote`	Footnote for the forest plot, will be aligned at left bottom of the plot. Please adjust the line length with line break to avoid the overlap with the arrow and/or x-axis.
`title`	The text for the title.
`nudge_y`	Horizontal adjustment to nudge groups by, must be within 0 to 1.
`fn_ci`	Name of the function to draw confidence interval, default is `makeci`. You can specify your own drawing function to draw the confidence interval, but the function needs to accept arguments `"est", "lower", "upper", "sizes", "xlim", "pch", "gp", "t_height", "nudge_y"`. Please refer to the `makeci` function for the details of these parameters.
`fn_summary`	Name of the function to draw summary confidence interval, default is `make_summary`. You can specify your own drawing function to draw the summary confidence interval, but the function needs to accept arguments `"est", "lower", "upper", "sizes", "xlim", "gp"`. Please refer to the `make_summary` function for the details of these parameters.
`index_args`	A character vector, name of the arguments used for indexing the row and column. This should be the name of the arguments that is working the same way as `est`, `lower` and `upper`. Check out the examples in the `make_boxplot`.
`theme`	Theme of the forest plot, see `forest_theme` for details.
`...`	Other arguments passed on to the `fn_ci` and `fn_summary`.

Value

A gtable object.

Examples

library(grid)
# Read provided sample example data
dt <- read.csv(system.file("extdata", "example_data.csv", package = "forestploter"))

# Keep needed columns
dt <- dt[,1:6]

# indent the subgroup if there is a number in the placebo column
dt$Subgroup <- ifelse(is.na(dt$Placebo),
                      dt$Subgroup,
                      paste0("   ", dt$Subgroup))

# NA to blank or NA will be transformed to carachter.
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

# Add blank column for the forest plot to display CI.
# Adjust the column width with space.
dt$` ` <- paste(rep(" ", 20), collapse = " ")

# 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))

# Define theme
tm <- forest_theme(base_size = 10,
                   refline_gp = gpar(col = "red"),
                   footnote_gp = gpar(col = "#636363", fontface = "italic"))

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),
            footnote = "This is the demo data. Please feel free to change\nanything you want.",
            theme = tm)

# Print plot
plot(p)
library(grid)
# Read provided sample example data
dt <- read.csv(system.file("extdata", "example_data.csv", package = "forestploter"))

# Keep needed columns
dt <- dt[,1:6]

# indent the subgroup if there is a number in the placebo column
dt$Subgroup <- ifelse(is.na(dt$Placebo),
                      dt$Subgroup,
                      paste0("   ", dt$Subgroup))

# NA to blank or NA will be transformed to carachter.
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

# Add blank column for the forest plot to display CI.
# Adjust the column width with space.
dt$` ` <- paste(rep(" ", 20), collapse = " ")

# 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))

# Define theme
tm <- forest_theme(base_size = 10,
                   refline_gp = gpar(col = "red"),
                   footnote_gp = gpar(col = "#636363", fontface = "italic"))

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),
            footnote = "This is the demo data. Please feel free to change\nanything you want.",
            theme = tm)

# Print plot
plot(p)

Forest plot default theme

Description

Default theme for the forest plot, but can pass other parameters. The parameters will be passed to corresponding elements of the forest plot.

ci_* Control the graphical parameters of confidence intervals
legend_* Control the graphical parameters of legend
xaxis_* Control the graphical parameters of x-axis
refline_* Control the graphical parameters of reference line
vertline_* Control the graphical parameters of vertical line
summary_* Control the graphical parameters of diamond shaped summary CI
footnote_* Control the graphical parameters of footnote
title_* Control the graphical parameters of title
arrow_* Control the graphical parameters of arrow

See gpar for more details.

Usage

forest_theme(
  base_size = 12,
  base_family = "",
  ci_pch = 15,
  ci_col = "black",
  ci_alpha = 1,
  ci_fill = NULL,
  ci_lty = 1,
  ci_lwd = 1,
  ci_Theight = NULL,
  legend_name = "Group",
  legend_position = "right",
  legend_value = "",
  legend_gp = gpar(fontsize = base_size, fontfamily = base_family, cex = 1),
  xaxis_gp = gpar(fontsize = base_size, fontfamily = base_family, lwd = 0.6, cex = 1),
  refline_gp = gpar(lwd = 1, lty = "dashed", col = "grey20"),
  vertline_lwd = 1,
  vertline_lty = "dashed",
  vertline_col = "grey20",
  summary_col = "#4575b4",
  summary_fill = summary_col,
  footnote_gp = gpar(fontsize = base_size, fontfamily = base_family, cex = 0.6, fontface
    = "plain", col = "black"),
  footnote_parse = TRUE,
  title_just = c("left", "right", "center"),
  title_gp = gpar(cex = 1.2, fontface = "bold", col = "black", fontfamily = base_family),
  arrow_type = c("open", "closed"),
  arrow_label_just = c("start", "end"),
  arrow_length = 0.05,
  arrow_gp = gpar(fontsize = base_size, fontfamily = base_family, lwd = 0.6),
  xlab_adjust = c("refline", "center"),
  xlab_gp = gpar(fontsize = base_size, fontfamily = base_family, cex = 1, fontface =
    "plain"),
  ...
)
forest_theme(
  base_size = 12,
  base_family = "",
  ci_pch = 15,
  ci_col = "black",
  ci_alpha = 1,
  ci_fill = NULL,
  ci_lty = 1,
  ci_lwd = 1,
  ci_Theight = NULL,
  legend_name = "Group",
  legend_position = "right",
  legend_value = "",
  legend_gp = gpar(fontsize = base_size, fontfamily = base_family, cex = 1),
  xaxis_gp = gpar(fontsize = base_size, fontfamily = base_family, lwd = 0.6, cex = 1),
  refline_gp = gpar(lwd = 1, lty = "dashed", col = "grey20"),
  vertline_lwd = 1,
  vertline_lty = "dashed",
  vertline_col = "grey20",
  summary_col = "#4575b4",
  summary_fill = summary_col,
  footnote_gp = gpar(fontsize = base_size, fontfamily = base_family, cex = 0.6, fontface
    = "plain", col = "black"),
  footnote_parse = TRUE,
  title_just = c("left", "right", "center"),
  title_gp = gpar(cex = 1.2, fontface = "bold", col = "black", fontfamily = base_family),
  arrow_type = c("open", "closed"),
  arrow_label_just = c("start", "end"),
  arrow_length = 0.05,
  arrow_gp = gpar(fontsize = base_size, fontfamily = base_family, lwd = 0.6),
  xlab_adjust = c("refline", "center"),
  xlab_gp = gpar(fontsize = base_size, fontfamily = base_family, cex = 1, fontface =
    "plain"),
  ...
)

Arguments

`base_size`	The size of text
`base_family`	The font family
`ci_pch`	Shape of the point estimation. It will be reused if the forest plot is grouped.
`ci_col`	Color of the CI. A vector of color should be provided for the grouped forest plot. An internal color set will be if only not.
`ci_alpha`	Scalar value, alpha channel for transparency of point estimation. A small vertical line will be added to indicate the point estimation if this is not equals to 1.
`ci_fill`	Color fill the point estimation. A vector of color should be provided for the grouped forest plot. If this is `NULL` (default), the value will inherit from `"ci_col"`. This is valid only if `ci_pch` within 15:25.
`ci_lty`	Line type of the CI. A vector of line type should be provided for the grouped forest plot.
`ci_lwd`	Line width of the CI. A vector of line type should be provided for the grouped forest plot.
`ci_Theight`	A unit specifying the height of the T end of CI. If set to `NULL` (default), no T end will be drawn.
`legend_name`	Title of the legend.
`legend_position`	Position of the legend, `"right"`, `"top"`, `"bottom"` or `"none"` to suppress the legend.
`legend_value`	Legend labels (expressions). A vector should be provided for the grouped forest plot. A "Group 1" etc will be created if not a vector for a grouped forest plot.
`legend_gp`	`gpar` graphical parameters of legend, see `gpar`.
`xaxis_gp`	`gpar` graphical parameters of x-axis, see `gpar`.
`refline_gp`	`gpar` graphical parameters of reference line, see `gpar`.
`vertline_lwd`	Line width for extra vertical line. A vector can be provided for each vertical line, and the values will be recycled if no enough values are given.
`vertline_lty`	Line type for extra vertical line. Works same as `vertline_lwd`.
`vertline_col`	Line color for the extra vertical line. Works same as `vertline_lwd`.
`summary_col`	Color for borders of the summary diamond shape.
`summary_fill`	Color for filling the summary diamond shape.
`footnote_gp`	`gpar` graphical parameters of footnote, see `gpar`.
`footnote_parse`	Parse footnote text (default).
`title_just`	The justification of the title, default is `'left'`.
`title_gp`	`gpar` graphical parameters of title, see `gpar`.
`arrow_type`	Type of the arrow below x-axis, see `arrow`.
`arrow_label_just`	The justification of the arrow label relative to arrow. Control the arrow label to align to the starting point of the arrow `"start"` (default) or the ending point of the arrow `"end"`.
`arrow_length`	The length of the arrow head, default is `0.05`. See `arrow`.
`arrow_gp`	`gpar` graphical parameters of arrow, see `gpar`.
`xlab_adjust`	Control the alignment of xlab to reference line (default) or center of the x-axis.
`xlab_gp`	`gpar` graphical parameters of xlab, see `gpar`.
`...`	Other parameters passed to table. See `tableGrob` for details.

Value

A list.

Get widths and height the forestplot

Description

get_wh can be used to find the correct width and height of the forestplot for saving, as the width and height is difficult to fit for saving.

Usage

get_wh(plot, unit = c("in", "cm", "mm"))
get_wh(plot, unit = c("in", "cm", "mm"))

Arguments

`plot`	A forest plot object.
`unit`	Unit of the plot size in `units` ("in", "cm", or "mm")to be saved.

Value

A named vector of width and height

Examples

## Not run: 
 dt <- read.csv(system.file("extdata", "example_data.csv", package = "forestploter"))
 dt <- dt[1:6,1:6]

 dt$` ` <- paste(rep(" ", 20), collapse = " ")

 p <- forest(dt[,c(1:3, 7)],
             est = dt$est,
             lower = dt$low,
             upper = dt$hi,
             ci_column = 4)

# get_wh example
p_wh <- get_wh(p)
pdf('test.pdf',width = p_wh[1], height = p_wh[2])
plot(p)
dev.off()

## End(Not run)
## Not run: 
 dt <- read.csv(system.file("extdata", "example_data.csv", package = "forestploter"))
 dt <- dt[1:6,1:6]

 dt$` ` <- paste(rep(" ", 20), collapse = " ")

 p <- forest(dt[,c(1:3, 7)],
             est = dt$est,
             lower = dt$low,
             upper = dt$hi,
             ci_column = 4)

# get_wh example
p_wh <- get_wh(p)
pdf('test.pdf',width = p_wh[1], height = p_wh[2])
plot(p)
dev.off()

## End(Not run)

Insert text to forest plot

Description

This function can be used to insert text to forest plot. Remember to adjust for the row number if you have added text before, including header. This is achieved by inserted new row(s) to the plot and will affect the row number. A text vector can be inserted to multiple columns or rows.

Usage

insert_text(
  plot,
  text,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  just = c("center", "left", "right"),
  before = TRUE,
  gp = gpar(),
  padding = unit(1, "mm"),
  parse = FALSE
)
insert_text(
  plot,
  text,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  just = c("center", "left", "right"),
  before = TRUE,
  gp = gpar(),
  padding = unit(1, "mm"),
  parse = FALSE
)

Arguments

`plot`	A forest plot object.
`text`	A character or expression vector, see `textGrob`.
`row`	Row to insert the text, this will be ignored if the `part` is "header".
`col`	A numeric value or vector indicating the columns the text will be added. The text will span over the column if a vector is given.
`part`	Part to insert text, body (default) or header.
`just`	The justification of the text, `"center"` (default), `"left"` or `"right"`.
`before`	Indicating the text will be inserted before or after the row.
`gp`	An object of class `"gpar"`, this is the graphical parameter settings of the text. See `gpar`.
`padding`	Padding of the text, default is `unit(1, "mm")`
`parse`	Logical, behaviour for parsing text as plotmath, see `plotmath`

Value

A gtable object.

Create horizontal boxplot grob

Description

Create horizontal boxplot grob

Usage

make_boxplot(
  est,
  lower,
  upper,
  lowhinge,
  uphinge,
  hinge_height = 0.2,
  pch,
  sizes = 1,
  gp = gpar(),
  gp_box = gp,
  t_height = NULL,
  xlim = c(0, 1),
  nudge_y = 0
)
make_boxplot(
  est,
  lower,
  upper,
  lowhinge,
  uphinge,
  hinge_height = 0.2,
  pch,
  sizes = 1,
  gp = gpar(),
  gp_box = gp,
  t_height = NULL,
  xlim = c(0, 1),
  nudge_y = 0
)

Arguments

`est`	Median value.
`lower`	Lower whisker.
`upper`	Upper whisker.
`lowhinge`	Lower hinge, a standard whisker will be drawn if this is missing.
`uphinge`	Upper hinge, a standard whisker will be drawn if this is missing.
`hinge_height`	Height of the hinge, default is 0.2.
`pch`	Numeric or character vector indicating what sort of plotting symbol to use. See `pointsGrob`.
`sizes`	Size of the point estimation box, can be a unit, vector or a list. Values will be used as it is, no transformation will be applied.
`gp`	Graphical parameters of `gpar`. Please refer to `forest_theme` for more details.
`gp_box`	Graphical parameters passed to the hinge, this will be passed to `rectGrob`. This does not support multiple groups.
`t_height`	Height of the whisker end vertices. If value is `NULL` (default), no vertices will be drawn.
`xlim`	Limits for the x axis as a vector of length 2, i.e. c(low, high).
`nudge_y`	Horizontal adjustment to nudge groups by, must be within 0 to 1.

Value

A gTree object

Examples

library(grid)

# Function to calculate Box plot values
box_func <- function(x){
  iqr <- IQR(x)
  q3 <- quantile(x, probs = c(0.25, 0.5, 0.75), names = FALSE)
  c("min" = q3[1] - 1.5*iqr, "q1" = q3[1], "med" = q3[2],
    "q3" = q3[3], "max" = q3[3] + 1.5*iqr)
}
# Prepare data
val <- split(ToothGrowth$len, list(ToothGrowth$supp, ToothGrowth$dose))
val <- lapply(val, box_func)

dat <- do.call(rbind, val)
dat <- data.frame(Dose = row.names(dat),
                  dat, row.names = NULL)

dat$Box <- paste(rep(" ", 20), collapse = " ")

# Draw single group box plot
tm <- forest_theme(ci_Theight = 0.2)

p <- forest(dat[,c(1, 7)],
            est = dat$med,
            lower = dat$min,
            upper = dat$max,
            # sizes = sizes,
            fn_ci = make_boxplot,
            ci_column = 2,
            lowhinge = dat$q1,
            uphinge = dat$q3,
            hinge_height = 0.2,
            index_args = c("lowhinge", "uphinge"),
            gp_box = gpar(fill = "black", alpha = 0.4),
            theme = tm
)
p

# Multiple group
# Prepare data
dat_oj <- dat[c(1, 3, 5),]
dat_vc <- dat[c(2, 4, 6), ]

dat <- data.frame(Dose = c(0.5, 1, 2))
dat$Box <- paste(rep(" ", 20), collapse = " ")

# Draw plot
tm <- forest_theme(ci_Theight = 0.2,
                   ci_pch = 3)

p <- forest(dat,
            est = list(dat_oj$med, dat_vc$med),
            lower = list(dat_oj$min, dat_vc$min),
            upper = list(dat_oj$max, dat_vc$max),
            fn_ci = make_boxplot,
            ci_column = 2,
            lowhinge = list(dat_oj$q1, dat_vc$q1),
            uphinge = list(dat_oj$q3, dat_vc$q3),
            hinge_height = 0.2,
            index_args = c("lowhinge", "uphinge"),
            theme = tm
)

p


library(grid)

# Function to calculate Box plot values
box_func <- function(x){
  iqr <- IQR(x)
  q3 <- quantile(x, probs = c(0.25, 0.5, 0.75), names = FALSE)
  c("min" = q3[1] - 1.5*iqr, "q1" = q3[1], "med" = q3[2],
    "q3" = q3[3], "max" = q3[3] + 1.5*iqr)
}
# Prepare data
val <- split(ToothGrowth$len, list(ToothGrowth$supp, ToothGrowth$dose))
val <- lapply(val, box_func)

dat <- do.call(rbind, val)
dat <- data.frame(Dose = row.names(dat),
                  dat, row.names = NULL)

dat$Box <- paste(rep(" ", 20), collapse = " ")

# Draw single group box plot
tm <- forest_theme(ci_Theight = 0.2)

p <- forest(dat[,c(1, 7)],
            est = dat$med,
            lower = dat$min,
            upper = dat$max,
            # sizes = sizes,
            fn_ci = make_boxplot,
            ci_column = 2,
            lowhinge = dat$q1,
            uphinge = dat$q3,
            hinge_height = 0.2,
            index_args = c("lowhinge", "uphinge"),
            gp_box = gpar(fill = "black", alpha = 0.4),
            theme = tm
)
p

# Multiple group
# Prepare data
dat_oj <- dat[c(1, 3, 5),]
dat_vc <- dat[c(2, 4, 6), ]

dat <- data.frame(Dose = c(0.5, 1, 2))
dat$Box <- paste(rep(" ", 20), collapse = " ")

# Draw plot
tm <- forest_theme(ci_Theight = 0.2,
                   ci_pch = 3)

p <- forest(dat,
            est = list(dat_oj$med, dat_vc$med),
            lower = list(dat_oj$min, dat_vc$min),
            upper = list(dat_oj$max, dat_vc$max),
            fn_ci = make_boxplot,
            ci_column = 2,
            lowhinge = list(dat_oj$q1, dat_vc$q1),
            uphinge = list(dat_oj$q3, dat_vc$q3),
            hinge_height = 0.2,
            index_args = c("lowhinge", "uphinge"),
            theme = tm
)

p

Create pooled summary diamond shape

Description

Create pooled summary diamond shape

Usage

make_summary(est, lower, upper, sizes = 1, gp, xlim, nudge_y = NULL)
make_summary(est, lower, upper, sizes = 1, gp, xlim, nudge_y = NULL)

Arguments

`est`	Point estimation. Can be a list for multiple columns and/or multiple groups. If the length of the list is larger than then length of `ci_column`, then the values reused for each column and considered as different groups.
`lower`	Lower bound of the confidence interval, same as `est`.
`upper`	Upper bound of the confidence interval, same as `est`.
`sizes`	Size of the point estimation box, can be a unit, vector or a list. Values will be used as it is, no transformation will be applied.
`gp`	Graphical parameters of `gpar`. Please refer to `forest_theme` for more details.
`xlim`	Limits for the x axis as a vector of length 2, i.e. c(low, high). It will take the minimum and maximum of the lower and upper value if not provided. This will apply to all CI columns if provided, and will be calculated automatically for each column if not provided. This should be a list with the same length of `ci_column` if different `xlim` for different column is desired.
`nudge_y`	Horizontal adjustment to nudge groups by, must be within 0 to 1.

Value

A gTree object

Create confidence interval grob

Description

Create confidence interval grob

Usage

makeci(
  est,
  lower,
  upper,
  pch,
  sizes = 1,
  gp = gpar(),
  t_height = NULL,
  xlim = c(0, 1),
  nudge_y = 0,
  name = NULL
)
makeci(
  est,
  lower,
  upper,
  pch,
  sizes = 1,
  gp = gpar(),
  t_height = NULL,
  xlim = c(0, 1),
  nudge_y = 0,
  name = NULL
)

Arguments

`est`	Point estimation. Can be a list for multiple columns and/or multiple groups. If the length of the list is larger than then length of `ci_column`, then the values reused for each column and considered as different groups.
`lower`	Lower bound of the confidence interval, same as `est`.
`upper`	Upper bound of the confidence interval, same as `est`.
`pch`	Numeric or character vector indicating what sort of plotting symbol to use. See `pointsGrob`.
`sizes`	Size of the point estimation box, can be a unit, vector or a list. Values will be used as it is, no transformation will be applied.
`gp`	Graphical parameters of `gpar`. Please refer to `forest_theme` for more details.
`t_height`	The height confidence interval line end vertices. If value is `NULL` (default), no vertices will be drawn.
`xlim`	Limits for the x axis as a vector of length 2, i.e. c(low, high). It will take the minimum and maximum of the lower and upper value if not provided. This will apply to all CI columns if provided, and will be calculated automatically for each column if not provided. This should be a list with the same length of `ci_column` if different `xlim` for different column is desired.
`nudge_y`	Horizontal adjustment to nudge groups by, must be within 0 to 1.
`name`	name of the grob.

Value

A gTree object

Draw plot

Description

Print or draw forestplot.

Usage

## S3 method for class 'forestplot'
print(x, autofit = FALSE, ...)

## S3 method for class 'forestplot'
plot(x, autofit = FALSE, ...)
## S3 method for class 'forestplot'
print(x, autofit = FALSE, ...)

## S3 method for class 'forestplot'
plot(x, autofit = FALSE, ...)

Arguments

`x`	forestplot to display
`autofit`	If true, the plot will be autofit.
`...`	other arguments not used by this method

Value

Invisibly returns the original forestplot.

`plot`	A forest plot object.
`row`	A numeric value or vector indicating row(s) to draw a grob.
`col`	A numeric value or vector indicating the columns to draw a grob.
`part`	The border will be added to `"body"` (default) or `"header"`.
`order`	Order in which the grobs should be plotted. Use `'top'` (default) to draw the grob above everything, `'text'` on the top of text given by plot data but below everything else, `'background'` plot on the top of background but below everything else, `'bottom'` below everything.
`gb_fn`	Grob function
`...`	Other parameters to be passed to `gb_fn`.

Package 'forestploter'

Help Index

Add border to cells

Description

Usage

Arguments

Value

See Also

Add grob in cells

Description

Usage

Arguments

Value

See Also

Add text to forest plot

Description

Usage

Arguments

Value

See Also

Edit forest plot

Description

Usage

Arguments

Value

See Also

Forest plot

Description

Usage

Arguments

Value

See Also

Examples

Forest plot default theme

Description

Usage

Arguments

Value

See Also

Get widths and height the forestplot

Description

Usage

Arguments

Value

Examples

Insert text to forest plot

Description

Usage

Arguments

Value

See Also

Create horizontal boxplot grob

Description

Usage

Arguments

Value

See Also

Examples

Create pooled summary diamond shape

Description

Usage

Arguments

Value

Create confidence interval grob

Description

Usage

Arguments

Value

Draw plot

Description

Usage

Arguments

Value