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

VolcanoPlotAtomic

R Documentation

Atomic volcano plot

Description

Atomic volcano plot

Usage

VolcanoPlotAtomic(
  data,
  x,
  y,
  ytrans = function(n) -log10(n),
  color_by = NULL,
  color_name = NULL,
  flip_negatives = FALSE,
  x_cutoff = NULL,
  y_cutoff = 0.05,
  trim = c(0, 1),
  xlim = NULL,
  x_cutoff_name = NULL,
  y_cutoff_name = NULL,
  x_cutoff_color = "red2",
  y_cutoff_color = "blue2",
  x_cutoff_linetype = "dashed",
  y_cutoff_linetype = "dashed",
  x_cutoff_linewidth = 0.5,
  y_cutoff_linewidth = 0.5,
  pt_size = 2,
  pt_alpha = 0.5,
  nlabel = 5,
  labels = NULL,
  label_size = 3,
  label_fg = "black",
  label_bg = "white",
  label_bg_r = 0.1,
  highlight = NULL,
  highlight_color = "red",
  highlight_size = 2,
  highlight_alpha = 1,
  highlight_stroke = 0.5,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  theme = "theme_this",
  theme_args = list(),
  palette = "Spectral",
  palcolor = NULL,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  seed = 8525,
  ...
)

Arguments

`data`	A data frame.
`x`	A character string specifying the column name of the data frame to plot for the x-axis.
`y`	A character string specifying the column name of the data frame to plot for the y-axis.
`ytrans`	A function to transform the y-axis values.
`color_by`	A character vector of column names to color the points by. If NULL, the points will be filled by the x and y cutoff value.
`color_name`	A character string to name the legend of color.
`flip_negatives`	A logical value to flip the y-axis for negative x values.
`x_cutoff`	A numeric value to set the x-axis cutoff. Both negative and positive of this value will be used.
`y_cutoff`	A numeric value to set the y-axis cutoff. Note that the y-axis cutoff will be transformed by `ytrans`. So you should provide the original value.
`trim`	A numeric vector of length 2 to trim the x-axis values. The values must be in the range from 0 to 1, which works as quantile to trim the x-axis values. For example, c(0.01, 0.99) will trim the 1% and 99% quantile of the x-axis values. If the values are less then 1% or greater than 99% quantile, the values will be set to the 1% or 99% quantile.
`xlim`	A numeric vector of length 2 to set the x-axis limits.
`x_cutoff_name`	A character string to name the x-axis cutoff. If "none", the legend for the x-axis cutoff will not be shown.
`y_cutoff_name`	A character string to name the y-axis cutoff. If "none", the legend for the y-axis cutoff will not be shown.
`x_cutoff_color`	A character string to color the x-axis cutoff line.
`y_cutoff_color`	A character string to color the y-axis cutoff line.
`x_cutoff_linetype`	A character string to set the x-axis cutoff line type.
`y_cutoff_linetype`	A character string to set the y-axis cutoff line type.
`x_cutoff_linewidth`	A numeric value to set the x-axis cutoff line size.
`y_cutoff_linewidth`	A numeric value to set the y-axis cutoff line size.
`pt_size`	A numeric value to set the point size.
`pt_alpha`	A numeric value to set the point transparency.
`nlabel`	A numeric value to set the number of labels to show. The points will be ordered by the distance to the origin. Top `nlabel` points will be labeled.
`labels`	A character vector of row names or indexes to label the points.
`label_size`	A numeric value to set the label size.
`label_fg`	A character string to set the label color.
`label_bg`	A character string to set the label background color.
`label_bg_r`	A numeric value specifying the radius of the background of the label.
`highlight`	A character vector of row names or indexes to highlight the points.
`highlight_color`	A character string to set the highlight color.
`highlight_size`	A numeric value to set the highlight size.
`highlight_alpha`	A numeric value to set the highlight transparency.
`highlight_stroke`	A numeric value to set the highlight stroke size.
`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.
`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).
`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.
`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.
`seed`	The random seed to use. Default is 8525.
`...`	Additional arguments.