VolcanoPlot

Generate a volcano plot based on differential expression analysis results.

Usage

VolcanoPlot(
  srt,
  group_by = NULL,
  test.use = "wilcox",
  DE_threshold = "avg_log2FC > 0 & p_val_adj < 0.05",
  x_metric = "diff_pct",
  palette = "RdBu",
  palcolor = NULL,
  pt.size = 1,
  pt.alpha = 1,
  cols.highlight = "black",
  sizes.highlight = 1,
  alpha.highlight = 1,
  stroke.highlight = 0.5,
  nlabel = 5,
  features_label = NULL,
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  label.size = 4,
  aspect.ratio = NULL,
  xlab = x_metric,
  ylab = "-log10(p-adjust)",
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE
)

Arguments

srt: An object of class Seurat containing the results of differential expression analysis.
group_by: A character vector specifying the column in srt to group the samples by. Default is NULL.
test.use: A character string specifying the type of statistical test to use. Default is "wilcox".
DE_threshold: A character string specifying the threshold for differential expression. Default is "avg_log2FC > 0 & p_val_adj < 0.05".
x_metric: A character string specifying the metric to use for the x-axis. Default is "diff_pct".
palette: A character string specifying the color palette to use for the plot. Default is "RdBu".
palcolor: A character string specifying the color for the palette. Default is NULL.
pt.size: A numeric value specifying the size of the points. Default is 1.
pt.alpha: A numeric value specifying the transparency of the points. Default is 1.
cols.highlight: A character string specifying the color for highlighted points. Default is "black".
sizes.highlight: A numeric value specifying the size of the highlighted points. Default is 1.
alpha.highlight: A numeric value specifying the transparency of the highlighted points. Default is 1.
stroke.highlight: A numeric value specifying the stroke width for the highlighted points. Default is 0.5.
nlabel: An integer value specifying the number of labeled points per group. Default is 5.
features_label: A character vector specifying the feature labels to plot. Default is NULL.
label.fg: A character string specifying the color for the labels' foreground. Default is "black".
label.bg: A character string specifying the color for the labels' background. Default is "white".
label.bg.r: A numeric value specifying the radius of the rounding of the labels' background. Default is 0.1.
label.size: A numeric value specifying the size of the labels. Default is 4.
aspect.ratio: A numeric value specifying the aspect ratio of the plot. Default is NULL.
xlab: A character string specifying the x-axis label. Default is the value of x_metric.
ylab: A character string specifying the y-axis label. Default is "-log10(p-adjust)".
theme_use: A character string specifying the theme to use for the plot. Default is "theme_scop".
theme_args: A list of theme arguments to pass to the theme_use function. Default is an empty list.
combine: A logical value indicating whether to combine the plots for each group into a single plot. Default is TRUE.
nrow: An integer value specifying the number of rows in the combined plot. Default is NULL.
ncol: An integer value specifying the number of columns in the combined plot. Default is NULL.
byrow: A logical value indicating whether to arrange the plots by row in the combined plot. Default is TRUE.

Examples

data("pancreas_sub")
# pancreas_sub <- RunDEtest(
#  pancreas_sub,
#  group_by = "CellType"
# )
VolcanoPlot(
  pancreas_sub,
  group_by = "CellType",
  ncol = 2
)

VolcanoPlot(
  pancreas_sub,
  group_by = "CellType",
  DE_threshold = "abs(diff_pct) > 0.3 & p_val_adj < 0.05",
  ncol = 2
)

VolcanoPlot(
  pancreas_sub,
  group_by = "CellType",
  x_metric = "avg_log2FC",
  ncol = 2
)

Usage

Arguments

See also

Examples