add p value and fold change on a plot
geom_compare(
mapping = NULL,
data = NULL,
stat = "compare",
position = "identity",
...,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE,
lab_pos = NULL,
step_increase = 0.1,
tip_length = 0.02,
lineend = "round",
cp_label = c("psymbol"),
ns_lineheight_just = 0.2,
ignore_ns = FALSE,
fc_method = NULL,
comparisons = NULL,
paired = FALSE,
alternative = "two.sided",
test_method = "wilcoxon",
ns_symbol = "NS",
cp_ref = NULL,
cp_inline = FALSE,
brackets_widen = 0,
fc_digits = 2,
cp_result = NULL,
cp_manual = NULL
)ggplot object
Set of aesthetic mappings created by aes(). If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
The data to be displayed in this layer. There are three options:
If NULL, the default, the data is inherited from the plot
data as specified in the call to ggplot().
A data.frame, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame, and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10)).
The statistical transformation to use on the data for this
layer, either as a ggproto Geom subclass or as a string naming the
stat stripped of the stat_ prefix (e.g. "count" rather than
"stat_count")
Position adjustment, either as a string naming the adjustment
(e.g. "jitter" to use position_jitter), or the result of a call to a
position adjustment function. Use the latter if you need to change the
settings of the adjustment.
Other arguments passed on to ggplot2::geom_segment().
If FALSE, the default, missing values are removed with
a warning. If TRUE, missing values are silently removed.
logical. Should this layer be included in the legends?
NA, the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display.
If FALSE, overrides the default aesthetics,
rather than combining with them. This is most useful for helper functions
that define both data and aesthetics and shouldn't inherit behaviour from
the default plot specification, e.g. borders().
position of the label brackets
the increase height for next bracket, a ratio according to the whole panel height
the length for tips at the ends of the brackets, a ratio according to the whole panel height
Line end style (round, butt, square).
which values will be add on the plot, a character vector
with some of psymbol, p, right_deno_fc, left_deno_fc in it.
If comparisons is assigned, you can also include fc1, fc2
if show psymbol in the label, justify
the NS labels to make the lineheights look balanced
if TRUE will ignore all label items if p >= 0.05,
or you can assign a character vector like cp_label to ignore some items
of the label
fold change method, default is mean. If you use log10 or
log2 axis, default is geom_mean.
a list of two-element vector, to assign the comparisons should be performed
paired test or not, FALSE as default. If TRUE, you should
use mapping=aes(paired_by=col) to indicate pairs by an extra column
one of two.sided, greater, less
wilcoxon as default, one of wilcoxon, t
the symbol of non-significant, NS as default
reference item, the others will be compared with it
draw in line or not, default is FALSE
widen the brackets, can be a negative value
fold change digits
comparation result tibble
manual comparisons table,
please refer to extract_compare()