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

VolcanoPlotAtomic

R Documentation

Atomic volcano plot (internal)

Description

Core implementation for drawing a single volcano plot. This is the workhorse behind the exported VolcanoPlot function — it takes a single data frame (no split_by support) and returns a ggplot object. The plot displays statistical significance (typically -log10 adjusted p-value) on the y-axis versus magnitude of change (log2 fold change) on the x-axis, with points coloured by significance category or a user-supplied variable. Top features can be automatically labelled via geom_text_repel(), and specific points can be highlighted.

The function categorises points into three groups based on cutoff thresholds: "sig_pos_x" (points exceeding both the positive x-cutoff and y-cutoff), "sig_neg_x" (points exceeding both the negative x-cutoff and y-cutoff), and "insig" (all remaining points). When color_by = NULL, this categorisation drives point colouring; otherwise the supplied column controls the colour scale.

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_by = 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,
  palreverse = FALSE,
  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 before plotting. The default `function(n) -log10(n)` converts p-values to a -log10 scale. The transformed values are used for both the y-axis and cutoff comparisons.
`color_by`	A character string specifying the column name to colour the points by. When `NULL` (default), points are automatically categorised as `"sig_pos_x"`, `"sig_neg_x"`, or `"insig"` based on `x_cutoff` and `y_cutoff`, and the colour legend is suppressed. When a column name is provided, the colour mapping follows the column type — discrete (character/factor) uses `scale_color_manual()` with the specified `palette`; numeric (continuous) uses `scale_color_gradientn()`.
`color_name`	A character string for the colour legend title when `color_by` is a numeric column. When `NULL` (default), the `color_by` column name is used.
`flip_negatives`	A logical value. When `TRUE`, y-values of points with negative x-values are multiplied by -1, creating a mirrored volcano plot where both up- and down-regulated features show their significance on the same side of the y-axis. A horizontal line at `y = 0` and absolute-value axis labels are added. Default: `FALSE`.
`x_cutoff`	A numeric value specifying the x-axis significance cutoff. Both the negative and positive of this value are used as vertical threshold lines. When `NULL` or `0`, no x-cutoff line is drawn. Default: `NULL`.
`y_cutoff`	A numeric value specifying the y-axis significance cutoff in the original (untransformed) scale. The value is transformed by `ytrans` before plotting. When `NULL`, no y-cutoff line is drawn and the category assignment uses only the x-cutoff. Default: `0.05`.
`trim`	A numeric vector of length 2 specifying quantile bounds for winsorizing the x-axis values. Values below the first quantile are clamped to that quantile; values above the second quantile are clamped to that quantile. Both values must be in `[0, 1]`. When both bounds are nonzero and of opposite sign, they are symmetrised to the smaller absolute value. Default: `c(0, 1)` (no trimming).
`xlim`	A numeric vector of length 2 to set the x-axis limits. Passed to `xlim()`. When `NULL` (default), limits are determined automatically from the data.
`x_cutoff_name`	A character string for the x-cutoff legend entry. When `"none"`, the legend for the x-cutoff line is suppressed entirely (the line is still drawn). When `NULL` (default), a label of the form `"<x> = +/-<value>"` is generated.
`y_cutoff_name`	A character string for the y-cutoff legend entry. When `"none"`, the legend for the y-cutoff line is suppressed entirely (the line is still drawn). When `NULL` (default), a label of the form `"<ylab> = <value>"` is generated.
`x_cutoff_color`	A character string specifying the colour of the x-axis cutoff line(s). Default: `"red2"`.
`y_cutoff_color`	A character string specifying the colour of the y-axis cutoff line(s). Default: `"blue2"`.
`x_cutoff_linetype`	A character string specifying the linetype of the x-axis cutoff line(s). Default: `"dashed"`.
`y_cutoff_linetype`	A character string specifying the linetype of the y-axis cutoff line(s). Default: `"dashed"`.
`x_cutoff_linewidth`	A numeric value specifying the linewidth of the x-axis cutoff line(s). Default: `0.5`.
`y_cutoff_linewidth`	A numeric value specifying the linewidth of the y-axis cutoff line(s). Default: `0.5`.
`pt_size`	A numeric value specifying the point size for all data points. Default: `2`.
`pt_alpha`	A numeric value in `[0, 1]` specifying the transparency of all data points. Default: `0.5`.
`nlabel`	An integer specifying the number of top features to label automatically. Points are ranked by Euclidean distance to the origin within each `sign(x)` group (and per facet level if `facet_by` is set). Only non-insignificant points receive labels. Default: `5`.
`labels`	A character vector of row names or integer indices specifying which points to label. Overrides automatic `nlabel` selection. When `NULL` (default), top `nlabel` points are chosen automatically.
`label_by`	A character string specifying the column whose values are used as label text. When `NULL` (default), row names of the data frame are used.
`label_size`	A numeric value specifying the font size of the labels. Default: `3`.
`label_fg`	A character string specifying the text colour of the labels. Default: `"black"`.
`label_bg`	A character string specifying the background colour of the label boxes (passed to `geom_text_repel(bg.color = ...)`). Default: `"white"`.
`label_bg_r`	A numeric value specifying the corner radius of the label background boxes (passed to `geom_text_repel(bg.r = ...)`). Default: `0.1`.
`highlight`	A character vector of row names or integer indices specifying which points to highlight with an overlaid point layer in `highlight_color`. When `NULL` (default), no highlighting is applied.
`highlight_color`	A character string specifying the colour of the highlight points. Default: `"red"`.
`highlight_size`	A numeric value specifying the point size of the highlight layer. Default: `2`.
`highlight_alpha`	A numeric value in `[0, 1]` specifying the transparency of the highlight points. Default: `1`.
`highlight_stroke`	A numeric value specifying the stroke width of the highlight point borders. Default: `0.5`.
`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).
`palreverse`	A logical value indicating whether to reverse the palette. Default is FALSE.
`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.

Value

A ggplot object with height and width attributes (in inches) attached.

Architecture

ggplot dispatch — selects gglogger::ggplot or ggplot2::ggplot based on getOption("plotthis.gglogger.enabled").
Input validation — trim (must be length-2 in [0, 1]) and xlim (must be length-2 or NULL) are validated via stopifnot(). trim is sorted.
Column resolution — x, y, color_by, facet_by, and label_by are validated and transformed via check_columns. Multi-column facet_by is concatenated with force_factor = TRUE.
y-axis transformation — the y-column is transformed by ytrans() (default: -log10(n)). The y_cutoff value is also transformed.
x_cutoff defaulting — if x_cutoff is NULL, it is set to 0 (suppressing the x-cutoff legend line).
Category assignment — a .category factor with levels c("sig_neg_x", "insig", "sig_pos_x") is created:
- When y_cutoff is non-NULL: points with |x| > x_cutoff AND y > y_cutoff are significant.
- When y_cutoff is NULL: only the x-cutoff determines significance.
Color resolution — three cases:
- color_by = NULL: uses .category as a discrete colour column; the legend is suppressed.
- Character/factor column: discrete colour scale via palette_this() and scale_color_manual(), guide suppressed.
- Numeric column: continuous gradient via scale_color_gradientn() with a framed colour-bar legend.
Flip negatives — when flip_negatives = TRUE, the y-values of points with negative x are multiplied by -1, creating a mirrored volcano where both up- and down-regulated features show their significance on the same side of the y-axis.
Label column — .label is populated from label_by or rownames(data).
Trim / winsorize — x-values beyond the trim quantile bounds are clamped. When both bounds are nonzero and of opposite sign, they are symmetrised to the smaller absolute value. Outlying points are marked in .outlier.
Label selection — two modes:
- Explicit labels: the specified rows (by name or index) are marked for labelling.
- Automatic: top nlabel points (by Euclidean distance to origin) are selected per sign(x) group, and per facet level if facet_by is set.
All labels are filtered to exclude "insig" points.
Data split — data is split into pos_data (x >= 0) and neg_data (x < 0) so that ggrepel labels can nudge in opposite directions (positive points nudge left, negative points nudge right).
Outlier jitter — outlier points are rendered separately with position_jitter() to reduce overplotting.
Base ggplot — geom_point() layers for positive, negative, and outlier data, with colour mapped to color_by.
Colour scale — discrete: scale_color_manual() with "insig" forced to "grey" (when palcolor is NULL); continuous: scale_color_gradientn() with palette re-scaled so that the colour-bar is centred at 0.
Highlight — when highlight is provided, two additional geom_point() layers (non-outliers and outliers with jitter) overlay the highlighted points in highlight_color.
x-cutoff lines — vertical dashed lines at +/- x_cutoff via geom_vline() with new_scale_color(), labelled by x_cutoff_name. Suppressed when x_cutoff is NULL or 0.
y-cutoff lines — horizontal dashed line(s) at y_cutoff (or +/- y_cutoff when flip_negatives = TRUE) via geom_hline() with new_scale_color(), labelled by y_cutoff_name.
Flip-negatives axis — when flip_negatives = TRUE, a solid geom_hline(yintercept = 0) is added and scale_y_continuous(labels = abs) formats the y-axis.
x-axis limits — optional xlim passed to ggplot2::xlim().
Reference line and labels — a grey80 dashed vertical line at x = 0, followed by geom_text_repel() for positive and negative labelled points with separate x-nudges.
Labels and theme — labs(), coord_cartesian(clip = "off"), do_call(theme, theme_args), and theme elements for aspect.ratio, legend.position, and legend.direction.
Dimension calculation — calculate_plot_dimensions() computes height and width attributes from base_height = 5, aspect.ratio, and legend geometry.
Faceting — facet_plot() wraps the plot with facet_wrap / facet_grid if facet_by is provided.