Make a shape plot with ggplot2

make_shape_plot(
  data,
  col.x = "x",
  col.estimate = "estimate",
  col.stderr = "stderr",
  col.lci = NULL,
  col.uci = NULL,
  col.n = NULL,
  exponentiate = FALSE,
  logscale = exponentiate,
  scalepoints = FALSE,
  minse = NA,
  pointsize = 3,
  col.group = NULL,
  shape = NULL,
  plotcolour = "black",
  colour = NULL,
  cicolour = colour,
  fill = NULL,
  ciunder = NULL,
  lines = FALSE,
  xlims,
  ylims,
  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,
  xbreaks = NULL,
  ybreaks = NULL,
  xlab = "Risk factor",
  ylab = "Estimate (95% CI)",
  legend.name = "",
  legend.position = "top",
  title = "Figure",
  printplot = TRUE,
  showcode = TRUE,
  addcode = NULL,
  addaes = NULL,
  addarg = 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)
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 will use shape 22 - squares with fill.)
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.
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)
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: "Figure")
printplot: Print the plot. (Default: TRUE)
showcode: Show the ggplot2 code to generate the plot in RStudio 'Viewer' pane. (Default: TRUE)
addcode: A character vector of code to add to the generated code. The first element should be a regular expression. The remaining elements are added to the generated code just before the first match of a line (trimmed of whitespace) with the regular expression. (Default: NULL)
addaes: Specify additional aesthetics for some ggplot layers.
addarg: Specify additional arguments for some ggplot layers.
envir: Environment in which to evaluate the plot code. May be useful when calling this function inside another function.

Value

A list:

plot: the plot
code: ggplot2 code to generate the plot