BoxViolinPlotAtomic: Atomic Box/Violin plot
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

BoxViolinPlotAtomic

R Documentation

Atomic Box/Violin plot

Description

Atomic Box/Violin plot

Usage

BoxViolinPlotAtomic(
  data,
  x,
  x_sep = "_",
  y = NULL,
  base = c("box", "violin"),
  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 = ifelse(isTRUE(flip) && isTRUE(stack), 90, 45),
  fill_mode = ifelse(!is.null(group_by), "dodge", "x"),
  fill_reverse = FALSE,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  add_point = FALSE,
  pt_color = "grey30",
  pt_size = NULL,
  pt_alpha = 1,
  y_nbreaks = 4,
  jitter_width = 0.5,
  jitter_height = 0.1,
  stack = FALSE,
  y_max = NULL,
  y_min = NULL,
  y_trans = "identity",
  add_box = FALSE,
  box_color = "black",
  box_width = 0.1,
  box_ptsize = 2.5,
  add_trend = FALSE,
  trend_color = NULL,
  trend_linewidth = 1,
  trend_ptsize = 2,
  add_stat = NULL,
  stat_name = NULL,
  stat_color = "black",
  stat_size = 1,
  stat_stroke = 1,
  stat_shape = 25,
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_line = NULL,
  line_color = "red2",
  line_width = 0.6,
  line_type = 2,
  highlight = NULL,
  highlight_color = "red2",
  highlight_size = 1,
  highlight_alpha = 1,
  comparisons = NULL,
  ref_group = NULL,
  pairwise_method = "wilcox.test",
  multiplegroup_comparisons = FALSE,
  multiple_method = "kruskal.test",
  sig_label = c("p.signif", "p.format"),
  sig_labelsize = 3.5,
  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.
`base`	A character string to specify the base plot type. Either "box" or "violin".
`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. Either "none", "mean_asc", "mean_desc", "mean", "median_asc", "median_desc", "median".
`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 of the column name to dodge the boxes/violins
`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.
`fill_mode`	A character string to specify the fill mode. Either "dodge", "x", "mean", "median".
`fill_reverse`	A logical value to reverse the fill colors for gradient fill (mean/median).
`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`	A numeric value specifying the transparency of the plot.
`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.
`add_point`	A logical value to add (jitter) points to the plot.
`pt_color`	A character string to specify the color of the points.
`pt_size`	A numeric value to specify the size of the points.
`pt_alpha`	A numeric value to specify the transparency of the points.
`y_nbreaks`	A numeric value to specify the number of breaks in the y-axis.
`jitter_width`	A numeric value to specify the width of the jitter.
`jitter_height`	A numeric value to specify the height of the jitter.
`stack`	A logical value whether to stack the facetted plot by 'facet_by'.
`y_max`	A numeric value or a character string to specify the maximum value of the y-axis.
`y_min`	A numeric value or a character string to specify the minimum value of the y-axis.
`y_trans`	A character string to specify the transformation of the y-axis.
`add_box`	A logical value to add box plot to the plot.
`box_color`	A character string to specify the color of the box plot.
`box_width`	A numeric value to specify the width of the box plot.
`box_ptsize`	A numeric value to specify the size of the box plot points in the middle.
`add_trend`	A logical value to add trend line to the plot.
`trend_color`	A character string to specify the color of the trend line.
`trend_linewidth`	A numeric value to specify the width of the trend line.
`trend_ptsize`	A numeric value to specify the size of the trend line points.
`add_stat`	A character string to add statistical test to the plot.
`stat_name`	A character string to specify the name of the stat legend.
`stat_color`	A character string to specify the color of the statistical test.
`stat_size`	A numeric value to specify the size of the statistical test.
`stat_stroke`	A numeric value to specify the stroke of the statistical test.
`stat_shape`	A numeric value to specify the shape of the statistical test.
`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_line`	A character string to add a line to the plot.
`line_color`	A character string to specify the color of the line.
`line_width`	A numeric value to specify the size of the line.
`line_type`	A numeric value to specify the type of the line.
`highlight`	A vector of character strings to highlight the points. It should be a subset of the row names of the data. If TRUE, it will highlight all points.
`highlight_color`	A character string to specify the color of the highlighted points.
`highlight_size`	A numeric value to specify the size of the highlighted points.
`highlight_alpha`	A numeric value to specify the transparency of the highlighted points.
`comparisons`	A logical value or a list of vectors to perform pairwise comparisons. If `TRUE`, it will perform pairwise comparisons for all pairs.
`ref_group`	A character string to specify the reference group for comparisons.
`pairwise_method`	A character string to specify the pairwise comparison method.
`multiplegroup_comparisons`	A logical value to perform multiple group comparisons.
`multiple_method`	A character string to specify the multiple group comparison method.
`sig_label`	A character string to specify the label of the significance test.
`sig_labelsize`	A numeric value to specify the size of the significance test label.
`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.