Help for package forestploter

Title:

Create a Flexible Forest Plot

Version:

1.1.3

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.

License:

MIT + file LICENSE

URL:

https://github.com/adayim/forestploter

BugReports:

https://github.com/adayim/forestploter/issues

Encoding:

UTF-8

RoxygenNote:

7.3.2

Imports:

grid, gridExtra, gtable

Suggests:

gridtext, rmarkdown, knitr, vdiffr, testthat (≥ 3.0.0), covr

VignetteBuilder:

knitr

Config/testthat/edition:

NeedsCompilation:

Packaged:

2025-04-13 15:38:18 UTC; alimd

Author:

Alimu Dayimu

[aut, cre]

Maintainer:

Alimu Dayimu <ad938@cam.ac.uk>

Repository:

CRAN

Date/Publication:

2025-04-13 16:00:07 UTC

forestploter: Create a Flexible Forest Plot

Description

Author(s)

Maintainer: Alimu Dayimu ad938@cam.ac.uk (ORCID)

Add border to cells

Description

Add border to any cells at any side.

add_underline is a wrapper of add_border can be used to add underline to cells.

Usage

add_border(
  plot,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  where = c("bottom", "left", "top", "right"),
  gp = gpar(lwd = 2)
)

add_underline(
  plot,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  gp = gpar(lwd = 2)
)

Arguments

plot

A forest plot object.

row

A numeric value or vector indicating row number to add border. This is corresponding to the data row number. Remember to account for any text inserted. A border will be drawn to all rows if this is omitted.

col

A numeric value or vector indicating the columns to add border. A border will be drawn to all columns if this is omitted.

part

The border will be added to "body" (default) or "header".

where

Where to draw the border of the cell, possible values are "bottom" (default), "left", "top" and "right"

gp

An object of class "gpar", graphical parameter to be passed to segmentsGrob.

Value

A gtable object.

Add grob in cells

Description

Draw grobs in any cells.

Usage

add_grob(
  plot,
  row = NULL,
  col = NULL,
  part = c("body", "header"),
  order = c("top", "text", "background", "bottom"),
  gb_fn,
  ...
)

Arguments

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.

Value

A gtable object.

Add text to forest plot

Description

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
)

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.

Checking error for forest plot

Description

Checking error for forest plot

Usage

check_errors(
  data,
  est,
  lower,
  upper,
  sizes,
  ref_line,
  vert_line,
  ci_column,
  is_summary,
  xlim,
  x_trans,
  ticks_at,
  ticks_digits,
  ticks_minor,
  title,
  arrow_lab,
  xlab
)

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.

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.

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.

title

The text for the title.

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.

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.

Edit forest plot

Description

This function is used to edit the graphical parameters 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(),
  ...
)

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,
  ...
)

Arguments

data

Data to be displayed in the forest plot

est

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

ticks_at

ticks_digits

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

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)

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),
  legend_ncol = 1,
  legend_byrow = TRUE,
  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.

legend_ncol

integer; the number of columns, see legendGrob.

legend_byrow

logical indicating whether rows of the legend are filled first, see legendGrob.

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"))

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)

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
)

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 legends

Description

This function used to create legends for the forest plot.

Usage

legend_grob(
  name = "",
  label,
  position = c("right", "top", "bottom"),
  hgap = unit(0.1, "lines"),
  vgap = unit(0.5, "lines"),
  pch = 15,
  ncol = 1,
  gp = gpar(lty = 1, col = "black", fill = "black", fontsize = 12, fontfamily = ""),
  byrow = TRUE,
  ...
)

Arguments

name

Character string, Legend name.

label

legend labels (expressions).

position

Position of the legend, "right", "top", "bottom".

hgap

Horizontal gap between the legend entries, see legendGrob for details.

vgap

Vertical gap between the legend entries, see legendGrob for details.

pch

Legend symbol.

ncol

integer; the number of columns

gp

Graphical parameters.

byrow

logical indicating whether rows of the legend are filled first.

...

Other parameters, not used currently.

Value

A frame grob

Make arrow

Description

Make arrow

Usage

make_arrow(x0 = 1, arrow_lab, arrow_gp, col_width, xlim, x_trans = "none")

Arguments

x0

Position of vertical line for 0 or 1.

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.

arrow_gp

Graphical parameters for arrow.

col_width

Width of the column arrow to be fitted.

xlim

x_trans

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
)

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

Create pooled summary diamond shape

Description

Create pooled summary diamond shape

Usage

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

Arguments

est

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

nudge_y

Horizontal adjustment to nudge groups by, must be within 0 to 1.

Value

A gTree object

Set x-axis ticks

Description

Create ticks points.

Usage

make_ticks(at = NULL, xlim, refline = 1, x_trans = "none")

Arguments

at

Numerical vector, create ticks at given values.

xlim

x_trans

Value

A vector

Create x-axis

Description

This function used to x-axis for the forest plot.

Usage

make_xaxis(
  at,
  at_minor = NULL,
  xlab = NULL,
  x0 = 1,
  x_trans = "none",
  ticks_digits = 1,
  gp = gpar(),
  xlab_gp = NULL,
  xlim
)

Arguments

at

Numerical vector, create ticks at given values.

at_minor

Numerical vector, create ticks at given values without label.

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.

x0

Position of vertical line for 0 or 1.

x_trans

ticks_digits

gp

Graphical parameters for arrow.

xlab_gp

Graphical parameters for xlab.

xlim

Value

A grob

Create xlim

Description

Create xlim based on value ranges.

Usage

make_xlim(
  xlim = NULL,
  lower,
  upper,
  ref_line = ifelse(x_trans %in% c("log", "log2", "log10"), 1, 0),
  ticks_at = NULL,
  x_trans = "none"
)

Arguments

xlim

lower

Lower bound of the confidence interval, same as est.

upper

Upper bound of the confidence interval, same as est.

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.

ticks_at

x_trans

Value

A list

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
)

Arguments

est

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

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, ...)

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.

Change Axis Scale: log2, log10 and more

Description

Change axis scale.

Usage

xscale(
  x,
  scale = c("none", "log", "log2", "log10", "scientific"),
  type = c("scale", "inv", "format"),
  format_digits = 1
)

Arguments

scale

axis scale. Allowed values are one of c("none", "log2", "log10", "sqrt", "percent", "dollar", "scientific"); e.g.: .scale="log2".

format_digits

Digits to keep while formatting

inv

Inverse value back to its original.

format

logical value. If TRUE, axis tick mark labels will be formatted when scale = "log2" or "log10".

forestploter: Create a Flexible Forest Plot

Description

Author(s)

See Also

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

Checking error for forest plot

Description

Usage

Arguments

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 legends

Description

Usage

Arguments

Value

Make arrow

Description

Usage

Arguments

Create horizontal boxplot grob

Description

Usage

Arguments

Value

See Also

Examples

Create pooled summary diamond shape

Description

Usage

Arguments

Value

Set x-axis ticks

Description