stat_ell: Plot confidence ellipse in 2D

In MAST: Model-based Analysis of Single Cell Transcriptomics

Description

The focus of the ellipse will be the point (x, y) and semi-major axes aligned with the coordinate axes and scaled by xse, yse and the level.

Usage

stat_ell(
  mapping = NULL,
  data = NULL,
  geom = "polygon",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  fill = NA,
  level = 0.95,
  lty = 2,
  invert = FALSE,
  alpha = 1,
  ...
)

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.
geom	The geometric object to use display the data
position	Position adjustment, either as a string, or the result of a call to a position adjustment function.
na.rm	If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.
show.legend	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.
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.
fill	A color or aesthetic mapping to fill color. Defaults to NA for empty ellipses.
level	The confidence level at which to draw an ellipse (default is level=0.95).
lty	The linetype to use. Can map to a variable. Defaults to 2 (dashed line)
invert	vector of length 1 that should either be "x","y",or TRUE. Specifies whether to plot the estimates from the discrete component on the inverse logit scale. invert specifies which axis to invert.
alpha	transparency
...	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.

Value

ggplot layer

Examples

data(vbetaFA)
library(ggplot2)
zlmCond <- zlm(~Stim.Condition, vbetaFA[1:10,])
MM <- model.matrix(~Stim.Condition,unique(colData(vbetaFA)[,c("Stim.Condition"),drop=FALSE]))
predicted <- predict(zlmCond,modelmatrix=MM)
plt <- ggplot(predicted)+aes(x=invlogit(etaD),y=muC,xse=seD,yse=seC,col=sample)+
   facet_wrap(~primerid,scales="free_y")+theme_linedraw()+
   geom_point(size=0.5)+scale_x_continuous("Proportion expression")+
   scale_y_continuous("Estimated Mean")+
   stat_ell(aes(x=etaD,y=muC),level=0.95, invert='x')
## plot with inverse logit transformed x-axis
print(plt)
# doesn't do anything in this case because there are no inestimable coefficients
predictI <- impute(predicted, groupby='primerid')

MAST documentation built on Nov. 8, 2020, 8:19 p.m.