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Volcano plot

Source: R/volcanoplot.R
VolcanoPlot.Rd

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,
  split_by = NULL,
  split_by_sep = "_",
  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,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  ...
)

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.

split_by

The column(s) to split data by and plot separately.

split_by_sep

The separator for multiple split_by columns. See split_by

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.

palcolor

A character string specifying the color to use in the palette.

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

Whether to combine the plots into one when facet is FALSE. Default is TRUE.

nrow

A numeric value specifying the number of rows in the facet.

ncol

A numeric value specifying the number of columns in the facet.

byrow

A logical value indicating whether to fill the plots by row.

...

Additional arguments.

Value

A list of ggplot objects or a wrap_plots object

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)
)
rownames(data) <- data$gene

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

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

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

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

VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", y_cutoff_name = "none",
   highlight = c("ANXA2", "TMEM40", "PF4", "GNG11", "CLU", "CD9", "FGFBP2",
   "TNFRSF1B", "IFI6"))