geom_cor: Add correlation and p-value to a ggplot2 plot

In lpantano/DEGreport: Report of DEG analysis

Add correlation and p-value to a ggplot2 plot

Description

geom_cor will add the correlatin, method and p-value to the plot automatically guessing the position if nothing else specidfied. family font, size and colour can be used to change the format.

Usage

geom_cor(
  mapping = NULL,
  data = NULL,
  method = "spearman",
  xpos = NULL,
  ypos = NULL,
  inherit.aes = TRUE,
  ...
)

Arguments

mapping	Set of aesthetic mappings created by aes() or 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.
data	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.
method	Method to calculate the correlation. Values are passed to cor.test(). (Spearman, Pearson, Kendall).
xpos	Locate text at that position on the x axis.
ypos	Locate text at that position on the y axis.
inherit.aes	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().
...	other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like color = "red" or size = 3. They may also be parameters to the paired geom/stat.

Details

It was integrated after reading this tutorial to extend ggplot2 layers

See Also

ggplot2::layer()

Examples

data(humanGender)
library(SummarizedExperiment)
library(ggplot2)
ggplot(as.data.frame(assay(humanGender)[1:1000,]),
       aes(x = NA20502, y = NA20504)) +
  geom_point() +
  ylim(0,1.1e5) +
  geom_cor(method = "kendall", ypos = 1e5) 

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.