ggpmisc (version 0.5.5)

scale_y_Pvalue: Convenience scale for P-values

Description

Scales for y aesthetic mapped to P-values as used in volcano plots with transcriptomics and metabolomics data.

Usage

scale_y_Pvalue(
  ...,
  name = expression(italic(P) - plain(value)),
  trans = NULL,
  breaks = NULL,
  labels = NULL,
  limits = c(1, 1e-20),
  oob = NULL,
  expand = NULL
)
scale_y_FDR(
  ...,
  name = "False discovery rate",
  trans = NULL,
  breaks = NULL,
  labels = NULL,
  limits = c(1, 1e-10),
  oob = NULL,
  expand = NULL
)
scale_x_Pvalue(
  ...,
  name = expression(italic(P) - plain(value)),
  trans = NULL,
  breaks = NULL,
  labels = NULL,
  limits = c(1, 1e-20),
  oob = NULL,
  expand = NULL
)
scale_x_FDR(
  ...,
  name = "False discovery rate",
  trans = NULL,
  breaks = NULL,
  labels = NULL,
  limits = c(1, 1e-10),
  oob = NULL,
  expand = NULL
)

Arguments

...

other named arguments passed to scale_y_continuous.

name

The name of the scale without units, used for the axis-label.

trans

Either the name of a transformation object, or the object itself. Use NULL for the default.

breaks

The positions of ticks or a function to generate them. Default varies depending on argument passed to log.base.labels.

labels

The tick labels or a function to generate them from the tick positions. The default is function that uses the arguments passed to log.base.data and log.base.labels to generate suitable labels.

limits

Use one of: NULL to use the default scale range, a numeric vector of length two providing limits of the scale; NA to refer to the existing minimum or maximum; a function that accepts the existing (automatic) limits and returns new limits.

oob

Function that handles limits outside of the scale limits (out of bounds). The default squishes out-of-bounds values to the boundary.

expand

Vector of range expansion constants used to add some padding around the data, to ensure that they are placed some distance away from the axes. The default is to expand the scale by 15% on each end for log-fold-data, so as to leave space for counts annotations.

Details

These scales only alter default arguments of scale_x_continuous() and scale_y_continuous(). Please, see documentation for scale_continuous for details.

See Also

Other Functions for quadrant and volcano plots: FC_format(), outcome2factor(), scale_colour_outcome(), scale_shape_outcome(), xy_outcomes2factor()

Examples

set.seed(12346)
my.df <- data.frame(x = rnorm(50, sd = 4),
                    y = 10^-runif(50, min = 0, max = 20))

ggplot(my.df, aes(x, y)) +
  geom_point() +
  scale_x_logFC() +
  scale_y_Pvalue()

ggplot(my.df, aes(x, y)) +
  geom_point() +
  scale_x_logFC() +
  scale_y_FDR(limits = c(NA, 1e-20))