| scale_colour_logFC {ggpmisc} | R Documentation |
Colour and fill scales for log fold change data
Description
Continuous scales for colour and fill aesthetics with defaults
suitable for values expressed as log2 fold change in data and
fold-change in tick labels. Supports tick labels and data expressed in any
combination of fold-change, log2 fold-change and log10 fold-change. Supports
addition of units to legend title passed as argument to the name
formal parameter.
Usage
scale_colour_logFC(
name = "Abundance of y%unit",
breaks = NULL,
labels = NULL,
limits = symmetric_limits,
oob = scales::squish,
expand = expansion(mult = 0.05, add = 0),
log.base.labels = FALSE,
log.base.data = 2L,
midpoint = NULL,
low.colour = "dodgerblue2",
mid.colour = "grey50",
high.colour = "red",
na.colour = "black",
aesthetics = "colour",
...
)
scale_color_logFC(
name = "Abundance of y%unit",
breaks = NULL,
labels = NULL,
limits = symmetric_limits,
oob = scales::squish,
expand = expansion(mult = 0.05, add = 0),
log.base.labels = FALSE,
log.base.data = 2L,
midpoint = NULL,
low.colour = "dodgerblue2",
mid.colour = "grey50",
high.colour = "red",
na.colour = "black",
aesthetics = "colour",
...
)
scale_fill_logFC(
name = "Abundance of y%unit",
breaks = NULL,
labels = NULL,
limits = symmetric_limits,
oob = scales::squish,
expand = expansion(mult = 0.05, add = 0),
log.base.labels = FALSE,
log.base.data = 2L,
midpoint = 1,
low.colour = "dodgerblue2",
mid.colour = "grey50",
high.colour = "red",
na.colour = "black",
aesthetics = "fill",
...
)
Arguments
name |
The name of the scale without units, used for the legend title. |
breaks |
The positions of ticks or a function to generate them. Default
varies depending on argument passed to |
labels |
The tick labels or a function to generate them from the tick
positions. The default is function that uses the arguments passed to
|
limits |
limits One of: NULL to use the default scale range from
ggplot2. A numeric vector of length two providing limits of the scale,
using NA to refer to the existing minimum or maximum. A function that
accepts the existing (automatic) limits and returns new limits. The default
is function |
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. |
log.base.labels, log.base.data |
integer or logical Base of logarithms used to
express fold-change values in tick labels and in |
midpoint |
numeric Value at the middle of the colour gradient, defaults to FC = 1, assuming data is expressed as logarithm. |
low.colour, mid.colour, high.colour, na.colour |
character Colour definitions to use for the gradient extremes and middle. |
aesthetics |
Character string or vector of character strings listing the name(s) of the aesthetic(s) that this scale works with. This can be useful, for example, to apply colour settings to the colour and fill aesthetics at the same time, via aesthetics = c("colour", "fill"). |
... |
other named arguments passed to |
Details
These scales only alter default arguments of
scale_colour_gradient2() and scale_fill_gradient2(). Please,
see documentation for scale_continuous for details.
The name argument supports the use of "%unit" at the end of the
string to automatically add a units string, otherwise user-supplied values
for names, breaks, and labels work as usual. Tick labels in the legend are
built based on the transformation already applied to the data (log2 by
default) and a possibly different log transformation (default is
fold-change with no transformation). The default for handling out of
bounds values is to "squish" them to the extreme of the scale, which is
different from the default used in 'ggplot2'.
See Also
Other scales for omics data:
outcome2factor(),
scale_shape_outcome(),
scale_x_logFC(),
xy_outcomes2factor()
Examples
set.seed(12346)
my.df <- data.frame(x = rnorm(50, sd = 4), y = rnorm(50, sd = 4))
# we assume that both x and y values are expressed as log2 fold change
ggplot(my.df, aes(x, y, colour = y)) +
geom_point(shape = "circle", size = 2.5) +
scale_x_logFC() +
scale_y_logFC() +
scale_colour_logFC()
ggplot(my.df, aes(x, y, fill = y)) +
geom_point(shape = "circle filled", colour = "black", size = 2.5) +
scale_x_logFC() +
scale_y_logFC() +
scale_fill_logFC()
my.labels <-
scales::trans_format(function(x) {log10(2^x)}, scales::math_format())
ggplot(my.df, aes(x, y, colour = y)) +
geom_point() +
scale_x_logFC(labels = my.labels) +
scale_y_logFC(labels = my.labels) +
scale_colour_logFC(labels = my.labels)
ggplot(my.df, aes(x, y, colour = y)) +
geom_point() +
scale_x_logFC(log.base.labels = 2) +
scale_y_logFC(log.base.labels = 2) +
scale_colour_logFC(log.base.labels = 2)
ggplot(my.df, aes(x, y, colour = y)) +
geom_point() +
scale_x_logFC(log.base.labels = 10) +
scale_y_logFC(log.base.labels = 10) +
scale_colour_logFC(log.base.labels = 10)
ggplot(my.df, aes(x, y, colour = y)) +
geom_point() +
scale_x_logFC(log.base.labels = 10) +
scale_y_logFC(log.base.labels = 10) +
scale_colour_logFC(log.base.labels = 10,
labels = FC_format(log.base.labels = 10,
log.base.data = 2L,
fmt = "% .*g"))
# override default arguments.
ggplot(my.df, aes(x, y, colour = y)) +
geom_point() +
scale_x_logFC() +
scale_y_logFC() +
scale_colour_logFC(name = "Change",
labels = function(x) {paste(2^x, "fold")})