Volcano Plot — VolcanoPlot • ggforge

A volcano plot is a type of scatter plot that shows statistical significance (usually on the y-axis) versus magnitude of change (usually on the x-axis).

Usage

VolcanoPlot(
  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,
  split_by = NULL,
  split_by_sep = "_",
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  theme = "theme_ggforge",
  theme_args = list(),
  palette = "Spectral",
  palcolor = NULL,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = NULL,
  guides = NULL,
  design = NULL,
  ...
)

Arguments

data: A data frame containing the data to plot
x: A character string of the column name to plot on the x-axis (e.g., log fold change).
y: A character string of the column name to plot on the y-axis (e.g., p-value).
ytrans: A function to transform the y-axis values. Default is -log10(n).
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.
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.
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_by: A character string of column name to use as labels. If NULL, the row names will be used.
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.
split_by: Column name(s) to split data into multiple plots
split_by_sep: Separator when concatenating multiple split_by columns
facet_by: Column name(s) for faceting the plot
facet_scales: Scales for facets: "fixed", "free", "free_x", "free_y"
facet_ncol: Number of columns in facet layout
facet_nrow: Number of rows in facet layout
facet_byrow: Fill facets by row (TRUE) or column (FALSE)
theme: Theme name (string) or theme function
theme_args: List of arguments passed to theme function
palette: Color palette name
palcolor: Custom colors for palette
title: Plot title
subtitle: Plot subtitle
xlab: X-axis label
ylab: Y-axis label
aspect.ratio: Aspect ratio of plot panel
legend.position: Legend position: "none", "left", "right", "bottom", "top"
legend.direction: Legend direction: "horizontal" or "vertical"
seed: Random seed for reproducibility
combine: Whether to combine split plots into one
nrow: Number of rows when combining plots
ncol: Number of columns when combining plots
byrow: Fill combined plots by row
axes: How to handle axes in combined plots ("keep", "collect", "collect_x", "collect_y")
axis_titles: How to handle axis titles in combined plots
guides: How to handle guides in combined plots ("collect", "keep", "auto")
design: Custom layout design for combined plots
...: Additional arguments passed to atomic plotting functions.

Value

A ggplot object or wrap_plots object or a list of ggplot objects

Examples

# \donttest{
set.seed(8525)
# Obtained by Seurat::FindMarkers 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,
    3.67, 4.79, 10.14, 5.36, 4.56, 4.62, 3.31, 4.72, 3.01, 3.86
  ),
  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, 8.93e-04, 9.61e-04, 1.47e-03, 4.35e-03,
    4.85e-03, 5.12e-03, 1.90e-02, 2.13e-02, 3.80e-02, 6.72e-02
  ),
  gene = c(
    "HLA-DPB1", "LYZ", "HLA-DRA", "TYMP", "HLA-DPA1", "HLA-DRB1", "CST3",
    "HLA-DQB1", "HLA-DRB5", "LST1", "CCL5", "LCK", "MS4A6A", "CD3D", "CD7",
    "CD3E", "CTSW", "GZMM", "GZMA", "IL32"
  ),
  group = sample(LETTERS[1:2], 20, replace = TRUE)
)

VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "-log10(0.05)")

VolcanoPlot(data,
  x = "avg_log2FC", y = "p_val_adj",
  label_by = "gene", y_cutoff_name = "-log10(0.05)"
)

VolcanoPlot(data,
  x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
  flip_negatives = TRUE, label_by = "gene"
)

VolcanoPlot(data,
  x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
  flip_negatives = TRUE, facet_by = "group", label_by = "gene"
)

VolcanoPlot(data,
  x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
  flip_negatives = TRUE, split_by = "group", label_by = "gene"
)

# }