Make a shape plot with ggplot2
Usage
shape_plot(
data,
col.x = "x",
col.estimate = c("estimate", "est", "beta", "loghr"),
col.stderr = c("stderr", "std.err", "se"),
col.lci = NULL,
col.uci = NULL,
col.n = NULL,
exponentiate = FALSE,
logscale = exponentiate,
scalepoints = FALSE,
digits = 2,
minse = NA,
pointsize = 3,
col.group = NULL,
shape = 15,
plotcolour = "black",
colour = plotcolour,
cicolour = colour,
fill = colour,
ciunder = NULL,
lines = FALSE,
xlims,
ylims,
height = NULL,
width = NULL,
gap = c(0.025, 0.025),
ext = c(0.025, 0.025),
ratio = 1.5,
base_size = 11,
base_line_size = base_size/22,
stroke = base_size/22,
axis.title.margin = 1,
xbreaks = NULL,
ybreaks = NULL,
xlab = "Risk factor",
ylab = "Estimate (95% CI)",
legend.name = "",
legend.position = "top",
title = NULL,
quiet = FALSE,
printplot = !quiet,
showcode = !quiet,
addaes = NULL,
addarg = NULL,
add = NULL,
envir = NULL
)Arguments
- data
The data frame containing estimates to be plotted.
- col.x
Name of column that provides the x-axis value (e.g. exposure, risk factor, dependent variable). (Default: "x")
- col.estimate
Name of column that provides point estimates. (Default: "estimate")
- col.stderr
Name of column that provides standard errors. (Default: "stderr")
- col.lci
Name of column that provides lower limit of confidence intervals.
- col.uci
Name of column that provides upper limit of confidence intervals.
- col.n
Name of column that provides number to be plotted below CIs.
- exponentiate
Exponentiate estimates (and CIs) before plotting, use log scale on the axis. (Default: FALSE)
- logscale
Use log scale for vertical axis. (Default: exponentiate)
- scalepoints
Should the points be scaled by inverse of the standard error? (Default: FALSE)
- digits
Number of digits to use in text of estimates.
- minse
Minimum standard error to use when scaling point size. (Default will use minimum in the data.)
- pointsize
The (largest) size of box to use for plotting point estimates. (Default: 3)
- col.group
Name of column that groups the estimates. (Default: NULL)
- shape
Shape of points. An integer, or name of a column of integers. (Default: 15)
- plotcolour
Colour for non-data aspects of the plot. (Default: "black")
- colour
Colour of points. Name of a colour, or name of a column of colour names. (Default will use plotcolour)
- cicolour
Colour of CI lines. Colour of CI lines. Name of a colour, or name of a column of colour names. (Default will use plotcolour)
- fill
Fill colour of points. Fill colour of points. Name of a colour, or name of a column of colour names. (Default will use plotcolour)
- ciunder
Plot CI lines before points. A logical value, or name of a column of logical values. (Default will plot CI lines after points.)
- lines
Plot lines (linear fit through estimates, weighted by inverse variance). (Default: FALSE)
- xlims
A numeric vector of length two. The limits of the x-axis.
- ylims
A numeric vector of length two. The limits of the y-axis.
- height
Panel height to use and apply different formatting to short CIs. A grid::unit() object, or if numeric is assumed to be in mm.
- width
Panel width.A grid::unit() object, or if numeric is assumed to be in mm.
- gap
A numeric vector of length two. The gap between plotting area and axis to the left and bottom of the plot, as a proportion of the x-axis length. (Default: c(0.025, 0.025))
- ext
A numeric vector of length two. The extensions to add to the right and top of the plot, as a proportion of the x-axis length. (Default: c(0.025, 0.025))
- ratio
The ratio (y-axis:x-axis) to use for the plot. (Default: 1.5)
- base_size
base font size, given in pts.
- base_line_size
base size for line elements
- stroke
Size of outline of shapes. (Default: base_size/22)
- axis.title.margin
Margin between axis titles and plot. (Default: 1)
- xbreaks
Breaks for the x axis. Passed to ggplots::scale_x_continuous. (Default: NULL)
- ybreaks
Breaks for the y axis. Passed to ggplots::scale_y_continuous. (Default: NULL)
- xlab
Label for x-axis. (Default: "Risk factor")
- ylab
Label for y-axis. (Default: "Estimate (95% CI)")
- legend.name
The name of the colour scale/legend for groups. (Default: "")
- legend.position
Position of the legend for groups ("none", "left", "right", "bottom", "top", or two-element numeric vector). (Default: "top")
- title
Plot title. (Default: NULL)
- quiet
Set to TRUE to not print the plot nor show generated code in the RStudio 'Viewer' pane. (Default: FALSE)
- printplot
Print the plot. (Default: !quiet)
- showcode
Show the ggplot2 code to generate the plot in RStudio 'Viewer' pane. (Default: !quiet)
- addaes, addarg, add
Methods for customising the plot. See documentation for details.
- envir
Environment in which to evaluate the plot code. May be useful when calling this function inside another function.