Plot a scatterplot to compare two contrasts

Usage

plotScatter.label(
  compare,
  df,
  label_x,
  label_y,
  lim.x,
  lim.y,
  color.palette,
  lab.genes = NULL,
  plot_all = "no",
  name.col = "geneid",
  lines = c("yes", "yes", "yes"),
  alpha = 1,
  size = 4,
  show.grid = "yes"
)

Arguments

compare: string, what values to plot? can be 'LFC' or 'P-adj'
df: data frame with LFC & padj values to plot from 2 contrasts
label_x: string, label for x-axis
label_y: string, label for y-axis
lim.x: x-axis limits
lim.y: y-axis limits
color.palette: character vector of colors to use for significance categories 'Both - same LFC sign', 'Both - opposite LFC sign', 'None', label_x, label_y
lab.genes: genes to label (default=NULL)
plot_all: string, can be 'yes' or 'no'. if 'yes', points outside axis limits are plotted along x/y axis lines (default='no').
name.col: gene name column to merge the 2 results, also used for labeling points
lines: 3-element character vector to plot gridlines in the order (x=0, y=0, x=y), with 'yes' or 'no' values. E.g. ('yes', 'yes', 'no') will plot dotted lines for x = 0 & y = 0, but not the x = y diagonal.
alpha: float, marker opacity (default=1).
size: float, marker size (default=4).
show.grid: string, can be 'yes' (default) or 'no'.

Value

ggplot handle