ScatterPlotAtomic: Scatter Plot Atomic
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

ScatterPlotAtomic

R Documentation

Scatter Plot Atomic

Description

Scatter Plot Atomic

Usage

ScatterPlotAtomic(
  data,
  x,
  y,
  size_by = 2,
  size_name = NULL,
  color_by = NULL,
  color_name = NULL,
  color_reverse = FALSE,
  theme = "theme_this",
  theme_args = list(),
  alpha = ifelse(shape %in% 21:25, 0.65, 1),
  shape = 21,
  border_color = "black",
  xtrans = "identity",
  ytrans = "identity",
  highlight = NULL,
  highlight_shape = 16,
  highlight_size = 3,
  highlight_color = "red",
  highlight_alpha = 1,
  palette = ifelse(!is.null(color_by) && !is.numeric(data[[color_by]]), "Paired",
    "Spectral"),
  palcolor = NULL,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  ...
)

Arguments

`data`	A data frame.
`x`	A character vector specifying the column to use for the x-axis. A numeric column is expected.
`y`	A character vector specifying the column to use for the y-axis. A numeric column is expected.
`size_by`	Which column to use as the size of the dots. It must be a numeric column. Or it can be a numeric value to specify the size of the dots.
`size_name`	A character vector specifying the name for the size legend.
`color_by`	Which column to use as the color of the dots. It could be a numeric column or a factor/character column. For shapes 21-25, the color is applied to the fill color.
`color_name`	A character vector specifying the name for the color legend.
`color_reverse`	A logical value indicating whether to reverse the color direction. Default is FALSE.
`theme`	A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".
`theme_args`	A list of arguments to pass to the theme function.
`alpha`	A numeric value specifying the transparency of the dots. Default is 1. For shapes 21-25, the transparency is applied to the fill color.
`shape`	A numeric value specifying the shape of the points. Default is 21.
`border_color`	A character vector specifying the color for the border of the points. Or TRUE to use the fill color as the border color.
`xtrans`	A character vector specifying the transformation of the x-axis. Default is "identity".
`ytrans`	A character vector specifying the transformation of the y-axis. Default is "identity".
`highlight`	A vector of indexes or rownames to select the points to highlight. It could also be an expression (in string) to filter the data.
`highlight_shape`	A numeric value specifying the shape of the highlighted points. Default is 16.
`highlight_size`	A numeric value specifying the size of the highlighted points. Default is 3.
`highlight_color`	A character vector specifying the color of the highlighted points. Default is "red".
`highlight_alpha`	A numeric value specifying the transparency of the highlighted points. Default is 1.
`palette`	A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different `split_by` values.
`palcolor`	A character string specifying the color to use in the palette. A named list can be used to specify the colors for different `split_by` values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).
`facet_by`	A character string specifying the column name of the data frame to facet the plot. Otherwise, the data will be split by `split_by` and generate multiple plots and combine them into one using `patchwork::wrap_plots`
`facet_scales`	Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See `ggplot2::facet_wrap`
`facet_ncol`	A numeric value specifying the number of columns in the facet. When facet_by is a single column and facet_wrap is used.
`facet_nrow`	A numeric value specifying the number of rows in the facet. When facet_by is a single column and facet_wrap is used.
`facet_byrow`	A logical value indicating whether to fill the plots by row. Default is TRUE.
`aspect.ratio`	A numeric value specifying the aspect ratio of the plot.
`legend.position`	A character string specifying the position of the legend. if `waiver()`, for single groups, the legend will be "none", otherwise "right".
`legend.direction`	A character string specifying the direction of the legend.
`title`	A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.
`subtitle`	A character string specifying the subtitle of the plot.
`xlab`	A character string specifying the x-axis label.
`ylab`	A character string specifying the y-axis label.
`...`	Additional arguments.