Volcanoplotter

Enables convenient visualization of differential expression data.

Usage

volcanoplotter(
  data,
  x_val,
  y_val,
  nonsig_col = "grey",
  pointsize = 1,
  point_alpha = 1,
  y_lab = "P-value",
  x_lab = "logFC",
  title = "",
  sig_neg_col = au_colors("blue"),
  sig_pos_col = au_colors("red"),
  pval_cutoff = 0.05,
  add_labels = FALSE,
  num_lab = 10,
  label_col = NA,
  lab_size = 3,
  dirs = "y",
  nudge_x1 = 10,
  nudge_x2 = -10,
  nudge_y1 = 0,
  nudge_y2 = 0,
  lab_bordersize = NA,
  fillcol = scales::alpha(c("white"), 0),
  brk = ggplot2::waiver(),
  lim = NULL,
  ...
)

Arguments

data

The data.frame to be used for the visualization.

x_val

string, the name of the column to plot on the x axis.

y_val

string, the name of the column to plot on the y axis.

nonsig_col

string, the color to use for the nonsignificant points. Default is grey.

pointsize

num, point size passed into geom_point(). Default is 1.

point_alpha

num, point opacity passed into geom_point(). Default is 1.

y_lab

string, the y axis label. Default is P-value.

x_lab

string, the x axis label. Default is logFC.

title

string, the title of the plot to be displayed on top. Default is "".

sig_neg_col

string, color to use for the significant negative points. Default is au_colors("blue").

sig_pos_col

string, color to use for the significant positive points. Default is au_colors("red").

pval_cutoff

num, significance cutoff. Default is 0.05.

add_labels

boolean, if TRUE, the number of points determined by num_lab are labelled. Default is FALSE.

num_lab

num, the number of points to label on the plot. Default is 10.

label_col

string, name of the column to use for labelling. Default is NA.

lab_size

num, size of the labels. Default is 3.

dirs

string, direction of position adjustment passed into geom_label_repel(). Possible values are x, y and both. Default is x.

nudge_x1

num, horizontal adjustment of the positive significant labels. Default is 10.

nudge_x2

num, horizontal adjustment of the negative significant labels. Default is -10.

nudge_y1

num, vertical adjustment of the positive significant labels. Default is 0.

nudge_y2

num, vertical adjustment of the negative significant labels. Default is 0.

lab_bordersize

num, width of the label border. Default is NA.

fillcol

string, background color for the labels. Default is transparent.

brk

vector, list of y-axis breaks.

lim

vector, y-axis limits.

...

other parameters passed into geom_label_repel().

Value

A ggplot object.

Examples

volcanoplotter(volcanodata, x_val = "logFC", y_val = "adj.P.Val",
add_labels = TRUE, label_col = "SYMBOL", num_lab = 5)