ggPoint: A ggplot-based dot plot wrapper function
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

ggPoint

R Documentation

A ggplot-based dot plot wrapper function

Description

This function is a wrapper around ggplot geom_point to allow for a more intuitive plotting of ArchR data.

Usage

ggPoint(
  x = NULL,
  y = NULL,
  color = NULL,
  discrete = TRUE,
  discreteSet = "stallion",
  continuousSet = "solarExtra",
  labelMeans = TRUE,
  pal = NULL,
  defaultColor = "lightGrey",
  highlightPoints = NULL,
  colorDensity = FALSE,
  size = 1,
  xlim = NULL,
  ylim = NULL,
  extend = 0.05,
  xlabel = "x",
  ylabel = "y",
  title = "",
  randomize = FALSE,
  seed = 1,
  colorTitle = NULL,
  colorOrder = NULL,
  colorLimits = NULL,
  alpha = 1,
  baseSize = 10,
  legendSize = 3,
  ratioYX = 1,
  labelAsFactors = TRUE,
  fgColor = "black",
  bgColor = "white",
  bgWidth = 1,
  labelSize = 3,
  addFit = NULL,
  rastr = FALSE,
  dpi = 300,
  ...
)

Arguments

`x`	A numeric vector containing the x-axis values for each point.
`y`	A numeric vector containing the y-axis values for each point.
`color`	A numeric/categorical vector used to determine the coloration for each point.
`discrete`	A boolean value indicating whether the supplied data is discrete (`TRUE`) or continuous (`FALSE`).
`discreteSet`	The name of a custom palette from `ArchRPalettes` to use for categorical/discrete color. This argument is only used if `discrete` is set to `TRUE`.
`continuousSet`	The name of a custom palette from `ArchRPalettes` to use for numeric color. This argument is only used if `discrete` is set to `FALSE`.
`labelMeans`	A boolean value indicating whether the mean of each categorical/discrete color should be labeled.
`pal`	A custom palette used to override discreteSet/continuousSet for coloring vector.
`defaultColor`	The default color for points that do not have another color applied (i.e. `NA` values).
`highlightPoints`	A integer vector describing which points to hightlight. The remainder of points will be colored light gray.
`colorDensity`	A boolean value indicating whether the density of points on the plot should be indicated by color. If `TRUE`, continuousSet is used as the color palette.
`size`	The numeric size of the points to be plotted.
`xlim`	A numeric vector of two values indicating the lower and upper bounds of the x-axis on the plot.
`ylim`	A numeric vector of two values indicating the lower and upper bounds of the y-axis on the plot.
`extend`	A numeric value indicating the fraction to extend the x-axis and y-axis beyond the maximum and minimum values if `xlim` and `ylim` are not provided. For example, 0.05 will extend the x-axis and y-axis by 5 percent on each end.
`xlabel`	The label to plot for the x-axis.
`ylabel`	The label to plot for the y-axis.
`title`	The title of the plot.
`randomize`	A boolean value indicating whether to randomize the order of the points when plotting.
`seed`	A numeric seed number for use in randomization.
`colorTitle`	A title to be added to the legend if `color` is supplied.
`colorOrder`	A vector that allows you to control the order of palette colors associated with the values in `color`. For example if you have `color` as `c("a","b","c")` and want to have the first color selected from the palette be used for "c", the second color for "b", and the third color for "a", you would supply the `colorOrder` as `c("c", "b", "a")`.
`colorLimits`	A numeric vector of two values indicating the lower and upper bounds of colors if numeric. Values beyond these limits are thresholded.
`alpha`	A number indicating the transparency to use for each point. See `ggplot2` for more details.
`baseSize`	The base font size (in points) to use in the plot.
`legendSize`	The size in inches to use for plotting the color legend.
`ratioYX`	The aspect ratio of the x and y axes on the plot.
`labelAsFactors`	A boolean indicating whether to label the `color` input as a numeric factor (`TRUE`) or with a character string (`FALSE`).
`fgColor`	The foreground color of the plot.
`bgColor`	The background color of the plot.
`bgWidth`	The background relative width size of the halos in the labeling.
`labelSize`	The numeric font size of labels.
`addFit`	A string indicating the method to use for adding a fit/regression line to the plot (see `ggplot2::geom_smooth()` methods). If set to `NULL`, no fit/regression line is added.
`rastr`	A boolean value that indicates whether the plot should be rasterized using `ggrastr`. This does not rasterize lines and labels, just the internal portions of the plot.
`dpi`	The resolution in dots per inch to use for the plot.