plot_forest: plot_forest
In omixVizR: A Toolkit for Omics Data Visualization

View source: R/plot_forest.R

plot_forest

R Documentation

plot_forest

Description

Creates a forest plot overlaid on a table.

Usage

plot_forest(
  p_left_data,
  point_estimate,
  ci_lower_bound,
  ci_upper_bound,
  ci_sep = ", ",
  p_right_data = NULL,
  precision_digits = 3,
  p_mid_width = 30,
  null_line_at = 1,
  output_path = NULL,
  dpi = 600,
  display = TRUE,
  font_family = c("MetroSans", "mono"),
  p_left_data_name = NULL,
  p_right_data_name = "Effect size (95% CI)",
  stripe_colour = "#eff3f2",
  background_colour = "white",
  x_scale_linear = TRUE,
  xlim = NULL,
  xbreaks = NULL,
  nudge_y = 0,
  nudge_x = 1,
  nudge_height = 0,
  nudge_width = 0,
  justify = 0,
  arrows = FALSE,
  arrow_labels = c("Lower", "Higher"),
  risk_colors = (ggsci::pal_npg("nrc"))(2),
  arrow_nudge_y = 0,
  add_plot = NULL,
  add_plot_width = 1,
  add_plot_gap = FALSE,
  point_sizes = 3,
  point_shapes = 16,
  p_mid_forest = NULL,
  lower_header_row = FALSE,
  render_as = "png",
  table_theme = NULL
)

Arguments

`p_left_data`	Data frame (required). The information to be displayed to the left of the forest plot.
`point_estimate`	Vector. The point estimates to be displayed in the forest plot.
`ci_lower_bound`	Vector. The lower confidence bounds.
`ci_upper_bound`	Vector. The upper confidence bounds.
`ci_sep`	String. What should separate the low and high confidence bounds? Default " to ".
`p_right_data`	Data frame (optional). Information to be displayed on the right side of the table. If not supplied, an Estimate column is generated automatically.
`precision_digits`	Integer. The number of decimal places on the point_estimate (default 3)
`p_mid_width`	Integer. The width of forest plot in characters (default 30)
`null_line_at`	Numeric. Default 1. Change to 0 if using absolute measures.
`output_path`	String. Where to save the image, default tempdir().
`dpi`	Numeric. The image resolution in dpi, default 600
`display`	Logical. Should the file be opened? Default TRUE.
`font_family`	String or character vector. The font to use for the ggplot and table. Default c("MetroSans", "mono"). The first available font is used.
`p_left_data_name`	String or String Vector. The name vector for the left side data. Default NULL, which uses the column names of p_left_data.
`p_right_data_name`	String. The name vector for the right side data. Default "Effect size (95% CI)"
`stripe_colour`	Hex String. Colour to use for the table stripes, default "#eff3f2".
`background_colour`	Hex String or Colour Name. The colour of the background, default "white".
`x_scale_linear`	Logical. Default TRUE, change to FALSE for a log scale.
`xlim`	Vector. Manually specify limits for the x axis as a vector length 2, i.e. c(low, high)
`xbreaks`	Vector. X axis breaks to label. Specify limits in xlim if using this option.
`nudge_y`	Numeric. Allows small changes to the vertical alignment of the forest plot points. 1 unit is approximately the height of 1 row.
`nudge_x`	Numeric. Nudge the alignment horizontally. Default 1. Higher values make the entire plot wider and consequently space out the elements of the figure.
`nudge_height`	Numeric. Adjust the overall height of the plot output. Default is 0.
`nudge_width`	Numeric. Adjust the overall width of the plot output. Default is 0.
`justify`	Numeric Vector. This should be a numeric vector either of length 1 (in which case it will apply to all columns) or of length equal to the number of columns in p_left_data + 1 (for the point_estimate column). Each number in the vector dictates the column justification, with 0 being left, 0.5 being center, and 1 being right.
`arrows`	Logical. Should there be arrows displayed below the ggplot? Default FALSE. Specify xlim if using arrows.
`arrow_labels`	String Vector, length 2. Labels for the arrows. Set arrows to TRUE or this will have no effect.
`risk_colors`	Vector. Length 2. Colors for the effect measure. Default is ggsci::pal_npg("nrc")(2).
`arrow_nudge_y`	Numeric. Nudge the vertical position of the arrows. Default 0.
`add_plot`	A ggplot object to add to the right side of the table. To align correctly with rows, 1 unit is the height of a row and y = 0 for the center of the bottom row.
`add_plot_width`	Numeric. Width to display add_plot. Relative to the width of the forest plot, where 1 (the default) is the same width.
`add_plot_gap`	Logical. Should there be space added between the plot and the main figure? Default FALSE.
`point_sizes`	Vector. Length should be equal to 1 or nrow(p_left_data). The sizes of the points in the center plot, where 3.25 is the default.
`point_shapes`	Vector. Length should be equal to 1 or nrow(p_left_data). The shapes of the points in the center plot, where 16 (a filled circle) is the default.
`p_mid_forest`	A ggplot object to use instead of the central plot.
`lower_header_row`	Logical. If TRUE, drops the header down one row (In the table rather than above it, like the default value (FALSE))
`render_as`	String or Function. What output format should be used? Option is passed to ggplot2::ggsave() as the argument "device". Either pass a device function (e.g. png) or one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only).
`table_theme`	A gridExtra table theme. If specified, overwrites all table theme customization in other options. The default is a modified version of ttheme_minimal.