VolcanoPlot: Volcano plot
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

VolcanoPlot

R Documentation

Volcano plot

Description

Produces a volcano plot — a scatter plot that displays statistical significance (typically -log10 adjusted p-value) on the y-axis versus magnitude of change (log2 fold change) on the x-axis. Points are coloured automatically by significance category ("sig_pos_x", "sig_neg_x", "insig") or by a user-supplied column. The most significant features can be labelled automatically via geom_text_repel(), and specific points can be highlighted.

The function supports automatic labelling of top features (by distance to origin), mirrored layout via flip_negatives, x-axis trimming to reduce the influence of extreme values, faceting, and splitting into separate sub-plots via split_by with per-split colour palette and legend control.

Usage

VolcanoPlot(
  data,
  x,
  y,
  ytrans = function(n) -log10(n),
  color_by = NULL,
  color_name = NULL,
  xlim = NULL,
  flip_negatives = FALSE,
  x_cutoff = NULL,
  y_cutoff = 0.05,
  split_by = NULL,
  split_by_sep = "_",
  label_by = 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,
  trim = c(0, 1),
  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,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)

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.
`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.
`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`.
`split_by`	The column(s) to split the data by and produce separate sub-plots. Multiple columns are concatenated with `split_by_sep`.
`split_by_sep`	A character string to separate concatenated `split_by` columns. Default `"_"`.
`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.
`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_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`.
`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).
`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.
`combine`	Logical; when `TRUE` (default), returns a combined `patchwork` object. When `FALSE`, returns a named list of individual `ggplot` objects.
`ncol`, `nrow`	Integer number of columns / rows for the combined layout (passed to `wrap_plots`).
`byrow`	Logical; fill the combined layout by row. Default `TRUE` (passed to `wrap_plots`).
`axes`	A character string specifying how axes should be treated across the combined layout (passed to `wrap_plots`).
`axis_titles`	A character string specifying how axis titles should be treated across the combined layout. Defaults to `axes`.
`guides`	A character string specifying how guides (legends) should be collected across panels. Default `"collect"` (passed to `combine_plots()`).
`design`	A custom layout design for the combined plot (passed to `combine_plots()`).
`...`	Additional arguments.

Value

A ggplot object, a patchwork object, or a named list of ggplot objects (when combine = FALSE), each with height and width attributes in inches.

split_by Workflow

When split_by is provided:

The split_by column(s) are validated via check_columns() with force_factor = TRUE and concat_multi = TRUE (multiple columns are concatenated with split_by_sep).
The data frame is split by split_by (preserving factor level order). If split_by is NULL, the data is wrapped in a single-element list with name "...".
Per-split palette, palcolor, legend.position, and legend.direction are resolved via check_palette(), check_palcolor(), and check_legend().
VolcanoPlotAtomic() is called for each split. If title is a function, it receives the split level name and can generate dynamic titles.
Results are combined via combine_plots() (when combine = TRUE) or returned as a named list.

Examples


set.seed(8525)
# Obtained by Seurat::FindMakers for the first cluster of pbmc_small
data <- data.frame(
   avg_log2FC = c(
     -3.69, -4.10, -2.68, -3.51, -3.09, -2.52, -3.53, -3.35, -2.82, -2.71, -3.16, -2.24,
     -5.62, -3.10, -3.42, -2.72, -3.23, -3.25, -4.68, 3.67, -2.66, 4.79, -2.99, 10.14,
     -1.78, -2.67, -2.26, -2.59, -3.39, 5.36, 4.56, 4.62, -2.94, -9.47, -9.12, -1.63,
     -2.77, 3.31, -1.53, -3.89, -4.21, 4.72, -2.98, -2.29, -1.41, -9.48, -4.30, 3.01,
     -1.19, -4.83, -1.35, -1.68, -1.63, -2.70, 3.86, 3.81, 7.23, -1.45, -0.92, -2.45,
     3.91, -4.45, -9.33, 3.56, 2.27, -1.60, -1.15, 11.40, -9.77, -8.32, 2.61, -1.25,
     -1.72, 10.61, 11.34, 10.02, 2.78, -3.48, -1.98, 5.86, 5.57, 4.57, 9.75, 9.97,
     10.90, 9.19, 2.93, 5.10, -1.52, -3.93, -1.95, -2.46, -0.64, 4.60, -1.82, -0.80,
     9.34, 7.51, 6.45, 5.23, 4.41, 3.60, -1.94, -1.15),
   p_val_adj = c(
     3.82e-09, 1.52e-07, 1.79e-07, 4.68e-07, 4.83e-07, 6.26e-07, 2.61e-06, 1.33e-05,
     1.79e-05, 3.71e-05, 5.21e-05, 5.36e-05, 5.83e-05, 6.66e-05, 8.22e-05, 2.89e-04,
     3.00e-04, 4.94e-04, 7.62e-04, 8.93e-04, 9.55e-04, 9.61e-04, 1.12e-03, 1.47e-03,
     1.66e-03, 1.95e-03, 2.06e-03, 3.01e-03, 3.26e-03, 4.35e-03, 4.85e-03, 5.12e-03,
     5.40e-03, 7.18e-03, 7.18e-03, 1.04e-02, 1.24e-02, 1.90e-02, 1.94e-02, 1.97e-02,
     2.09e-02, 2.13e-02, 2.25e-02, 2.61e-02, 3.18e-02, 3.27e-02, 3.69e-02, 3.80e-02,
     4.95e-02, 5.73e-02, 5.77e-02, 6.10e-02, 6.22e-02, 6.31e-02, 6.72e-02, 9.23e-02,
     9.85e-02, 1.06e-01, 1.07e-01, 1.11e-01, 1.31e-01, 1.38e-01, 1.40e-01, 1.43e-01,
     2.00e-01, 2.39e-01, 2.49e-01, 2.57e-01, 2.86e-01, 2.86e-01, 2.98e-01, 3.32e-01,
     4.15e-01, 4.91e-01, 4.91e-01, 4.91e-01, 5.97e-01, 7.11e-01, 7.59e-01, 8.38e-01,
     9.20e-01, 9.20e-01, 9.29e-01, 9.29e-01, 9.29e-01, 9.29e-01, 9.34e-01, 9.68e-01,
     1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00,
     1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00),
   gene = c(
     "HLA-DPB1", "LYZ", "HLA-DRA", "TYMP", "HLA-DPA1", "HLA-DRB1", "CST3", "HLA-DQB1",
     "HLA-DRB5", "LST1", "HLA-DQA1", "AIF1", "S100A8", "IFITM3", "HLA-DMB", "FCGRT",
     "SERPINA1", "IFI30", "S100A9", "CCL5", "GRN", "LCK", "HLA-DMA", "MS4A6A", "CTSS",
     "CFP", "FCN1", "BID", "CFD", "CD3D", "CD7", "CD3E", "LGALS2", "CD14", "SMCO4",
     "LINC00936", "HCK", "CTSW", "LGALS1", "HLA-DQA2", "LRRC25", "GZMM", "RNF130",
     "LGALS3", "S100A11", "C5AR1", "IL1B", "GZMA", "FCER1G", "MPEG1", "TYROBP", "TSPO",
     "GSTP1", "CTSB", "IL32", "CD247", "GNLY", "COTL1", "NFKBIA", "NUP214", "LAMP1",
     "FPR1", "CLEC10A", "CST7", "PRF1", "BLVRA", "PSAP", "GZMH", "EAF2", "ASGR1",
     "RARRES3", "SAT1", "LY86", "GP9", "TUBB1", "NGFRAP1", "XBP1", "SCO2", "RGS2", "GZMB",
     "HIST1H2AC", "KLRD1", "PGRMC1", "AKR1C3", "PTGDR", "IL2RB", "GYPC", "CCL4", "CD68",
     "FCER1A", "CD79B", "MS4A7", "CARD16", "ACAP1", "CD79A", "ANXA2", "TMEM40", "PF4",
     "GNG11", "CLU", "CD9", "FGFBP2", "TNFRSF1B", "IFI6"),
  pct_diff = c(
     -0.752, -0.457, -0.460, -0.671, -0.626, -0.701, -0.502, -0.619, -0.623, -0.598,
     -0.566, -0.626, -0.543, -0.566, -0.541, -0.542, -0.515, -0.489, -0.444, 0.428,
     -0.517, 0.461, -0.491, -0.410, -0.480, -0.491, -0.521, -0.491, -0.438, 0.411,
     0.411, 0.409, -0.438, -0.359, -0.359, -0.440, -0.386, 0.385, -0.332, -0.361, -0.361,
     0.364, -0.387, -0.415, -0.454, -0.308, -0.335, 0.364, -0.454, -0.309, -0.379, -0.427,
     -0.377, -0.389, 0.335, 0.315, 0.313, -0.284, -0.502, -0.309, 0.313, -0.284, -0.256,
     0.309, 0.313, -0.364, -0.406, 0.244, -0.231, -0.231, 0.281, -0.311, -0.312, 0.220,
     0.220, 0.220, 0.261, -0.232, -0.367, 0.240, 0.218, 0.218, 0.195, 0.195, 0.195, 0.195,
     0.262, 0.218, -0.288, -0.207, -0.290, -0.233, -0.367, 0.217, -0.233, -0.403, 0.171,
     0.194, 0.194, 0.194, 0.194, 0.213, -0.235, -0.292),
  group = sample(LETTERS[1:2], 104, replace = TRUE)
)
# If set, it will be used as labels if label_by is not set.
# rownames(data) <- data$gene

# --- Basic usage ---
VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", color_by = "pct_diff",
   y_cutoff_name = "-log10(0.05)")
# --- With gene labels ---
VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", color_by = "pct_diff",
   y_cutoff_name = "-log10(0.05)", label_by = "gene")
# --- Mirrored layout ---
VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
   flip_negatives = TRUE, label_by = "gene")
# --- With faceting ---
VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
   flip_negatives = TRUE, facet_by = "group", label_by = "gene")
# --- With splitting ---
VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
   flip_negatives = TRUE, split_by = "group", label_by = "gene")
# --- With highlighting ---
VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
   highlight = c("ANXA2", "TMEM40", "PF4", "GNG11", "CLU", "CD9", "FGFBP2",
   "TNFRSF1B", "IFI6"), label_by = "gene")
# --- Per-split palettes ---
VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", color_by = "pct_diff",
   y_cutoff_name = "-log10(0.05)", split_by = "group", label_by = "gene",
   palette = c(A = "Set1", B = "Dark2"))

plotthis documentation built on July 9, 2026, 5:07 p.m.