ggcyto_par_set: Set some default parameters for ggcyto

In RGLab/ggcyto: Visualize Cytometry data with ggplot

Set some default parameters for ggcyto

Description

Use this function to modify ggcyto parameters These are the regular (or to be instantiated as) scales, labs, facet objects. They can be added as a single layer to the plot for the convenience.

Usage

ggcyto_par_set(...)

Arguments

...	a list of element name, element pairings that modify the existing parameter settings

Value

a list of new settings for ggycto

elements

The individual elements are:

limits	can be "data"(default) or "instrument" or a list of numeric limits for x and y (e.g. list(x = c(0, 4000)))
facet	the regular facet object
hex_fill	default scale_fill_gradientn for geom_hex layer
lab	labs_cyto object

Examples

library(ggcyto)
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))

p <- ggcyto(gs, aes(x = CD4, y = CD8), subset = "CD3+") 
# 2d plot 
p <- p + geom_hex(bins = 64)
p

#use instrument range by overwritting the default limits settings
p + ggcyto_par_set(limits = "instrument")

#manually set limits
myPars <- ggcyto_par_set(limits = list(x = c(0,3.2e3), y = c(-10, 3.5e3)))
 p  + myPars# or xlim(0,3.2e3) + ylim(-10, 3.5e3) 

RGLab/ggcyto documentation built on March 3, 2024, 6:23 p.m.