JitterPlotAtomic: Atomic Jitter plot
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

JitterPlotAtomic

R Documentation

Atomic Jitter plot

Description

Atomic Jitter plot

Usage

JitterPlotAtomic(
  data,
  x,
  x_sep = "_",
  y = NULL,
  in_form = c("long", "wide"),
  sort_x = c("none", "mean_asc", "mean_desc", "mean", "median_asc", "median_desc",
    "median"),
  flip = FALSE,
  keep_empty = FALSE,
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  x_text_angle = 0,
  order_by = "-({y}^2 + {size_by}^2)",
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  shape = 21,
  border = "black",
  size_by = 2,
  size_name = NULL,
  size_trans = NULL,
  y_nbreaks = 4,
  jitter_width = 0.5,
  jitter_height = 0,
  y_max = NULL,
  y_min = NULL,
  y_trans = "identity",
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_hline = NULL,
  hline_type = "solid",
  hline_width = 0.5,
  hline_color = "black",
  hline_alpha = 1,
  labels = NULL,
  label_by = NULL,
  nlabel = 5,
  label_size = 3,
  label_fg = "black",
  label_bg = "white",
  label_bg_r = 0.1,
  highlight = NULL,
  highlight_color = "red2",
  highlight_size = 1,
  highlight_alpha = 1,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  ...
)

Arguments

`data`	A data frame.
`x`	A character string of the column name to plot on the x-axis. A character/factor column is expected. If multiple columns are provided, the columns will be concatenated with `x_sep`.
`x_sep`	A character string to concatenate the columns in `x`, if multiple columns are provided. When `in_form` is "wide", `x` columns will not be concatenated.
`y`	A character string of the column name to plot on the y-axis. A numeric column is expected. When `in_form` is "wide", `y` is not required. The values under `x` columns will be used as y-values.
`in_form`	A character string to specify the input data type. Either "long" or "wide".
`sort_x`	A character string to specify the sorting of x-axis, chosen from "none", "mean_asc", "mean_desc", "mean", "median_asc", "median_desc", "median". `none` means no sorting (as-is). `mean_asc` sorts the x-axis by ascending mean of y-values. `mean_desc` sorts the x-axis by descending mean of y-values. `mean` is an alias for `mean_asc`. `median_asc` sorts the x-axis by ascending median of y-values. `median_desc` sorts the x-axis by descending median of y-values. `median` is an alias for `median_asc`.
`flip`	A logical value to flip the plot.
`keep_empty`	A logical value to keep the empty levels in the x-axis.
`group_by`	A character string to dodge the points.
`group_by_sep`	A character string to concatenate the columns in `group_by`, if multiple columns are provided.
`group_name`	A character string to name the legend of dodge.
`x_text_angle`	A numeric value specifying the angle of the x-axis text.
`order_by`	A string of expression passed to `dplyr::arrange()` to order the data to get the top `nlabel` points for labeling. Default is `-({y}^2 + {size_by}^2)` (similar to VolcanoPlot).
`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.
`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).
`alpha`	Point transparency.
`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.
`shape`	A numeric value to specify the point shape. Shapes 21–25 have borders; border behavior is controlled by `border`.
`border`	A logical or character value to specify the border of points when the shape has border (21–25). If TRUE, border color follows the point color (same as fill). If a color string, uses that constant border color. If FALSE, no border.
`size_by`	A numeric column name or a single numeric value for the point size. When a column, sizes are scaled (see scatter plots).
`size_name`	Legend title for size when `size_by` is a column.
`size_trans`	A function or a name of a global function to transform `size_by` (when `size_by` is a column). The legend shows original (untransformed) values.
`jitter_width`, `jitter_height`	Jitter parameters.
`y_max`, `y_min`	Numeric or quantile strings ("q95", "q5") for y limits computation (used for fixed coord).
`y_trans`, `y_nbreaks`	Axis settings.
`add_bg`	A logical value to add background to the plot.
`bg_palette`	A character string to specify the palette of the background.
`bg_palcolor`	A character vector to specify the colors of the background.
`bg_alpha`	A numeric value to specify the transparency of the background.
`add_hline`	Add one or more horizontal reference lines at the given y-value(s).
`hline_type`	The line type for the horizontal reference line(s).
`hline_width`	The line width for the horizontal reference line(s).
`hline_color`	The color for the horizontal reference line(s).
`hline_alpha`	The alpha for the horizontal reference line(s).
`labels`	A vector of row names or indices to label the points.
`label_by`	A character column name to use as the label text. If NULL, rownames are used.
`nlabel`	Number of points to label per x-group when `labels` is NULL (top by y^2 + size^2).
`label_size`, `label_fg`, `label_bg`, `label_bg_r`	Label aesthetics.
`highlight`, `highlight_color`, `highlight_size`, `highlight_alpha`	Highlighted point options.
`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.
`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.
`seed`	The random seed to use. Default is 8525.
`...`	Additional arguments.