overlayLegend: overlay a clone size legend on an APackOfTheClones plot

In APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

overlay a clone size legend on an APackOfTheClones plot

Description

This function has most of the parameters related to legend in APOTCPlot(), and can plot a new / override the current legend. However, it is very important that the input plot to the function is a plot generated solely by APOTCPlot() or vizAPOTC() due to it being a custom ggplot object. It will not override or erase any additional layers that the user/other functions have added. To just remove the legend, see removeLegend.

Usage

overlayLegend(
  apotc_ggplot,
  legend_sizes = "auto",
  legend_position = "auto",
  legend_buffer = 0.2,
  legend_color = "#808080",
  legend_spacing = "auto",
  legend_label = "Clone sizes",
  legend_text_size = 5,
  add_legend_background = TRUE,
  add_legend_centerspace = 0,
  linetype = "blank",
  res = 360L
)

Arguments

apotc_ggplot	a ggplot object that is the output of APOTCPlot() or vizAPOTC()
legend_sizes	numeric vector. Indicates the circle sizes to be displayed on the legend, and will always be sorted from smallest to greatest. Defaults to "auto" which estimate a reasonable range of sizes to display.
legend_position	character or numeric. Can be set to either "top_left", "top_right", "bottom_left", "bottom_right" and places the legend roughly in the corresponding position. Otherwise, can be a numeric vector of length 2 indicating the x and y position of the topmost (smallest) circle of the legend.
legend_buffer	numeric. Indicates how much to "push" the legend towards the center of the plot from the selected corner. If negative, will push away
legend_color	character. Indicates the hex color of the circles displayed on the legend. Defaults to the hex code for a gray tone
legend_spacing	numeric. Indicates the horizontal distance between each stacked circle on the size legend. Defaults to "auto" which will use an estimated value depending on plot size
legend_label	character. The title of the legend, which defaults to ⁠"clone sizes⁠.
legend_text_size	numeric. The text size of the letters and numbers on the legend
add_legend_background	logical. If TRUE, will add a border around the legend and fill the background to be white, overlaying anything else.
add_legend_centerspace	numeric. An additional amount of distance changed between the circle sizes on the left side of the legend and the numbers on the right. Useful to set to around 0.5 (or more / less) when there are particularly large clone sizes that may cover the numbers.
linetype	The type of outline each circle should have. defaults to ⁠"blank⁠ meaning no outline. More information is in the function documentation of ggforce::geom_circle.
res	The number of points on the generated path per full circle. From plot viewers, if circles seem slightly too pixelated, it is recommended to first try to export the plot as an .svg before increasing res due to increased plotting times from ggforce::geom_circle.

Details

The size legend on APackOfTheClones plots are simply a collection of annotation layers of the rect, text, circle geoms. Therefore it isn't quite a ggplot legend. In the actual ggplot object, the ⁠$layers⁠ element should all be named with an empty character "", and those that comprise the annotation layers of the legend should be named whatever APackOfTheClones:::.ApotcLegendLayerName is. Note that this is simply an implementation detail that the user should not interfere with.

Value

A ggplot object of the APackOfTheClones clonal expansion plot of the seurat object. There is an additional 10th element in the object named "APackOfTheClones" used by other functions in this package and shouldn't interfere with any other ggplot functionality. (As far as currently known)

See Also

removeLegend

Examples

library(dplyr)

# create a plot with a legend
apotc_plot <- vizAPOTC(get(data("combined_pbmc")), verbose = FALSE)

# reposition the legend to top right
overlayLegend(apotc_plot, legend_position = "top right")

# use different sizes and label - may be nice to use the pipe
apotc_plot %>% overlayLegend(
    legend_sizes = c(1, 3, 7, 9),
    legend_label = "odd sizes"
)

APackOfTheClones documentation built on Oct. 11, 2024, 1:08 a.m.