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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(ggcyto)
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: flowViz
Loading required package: lattice
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ggcyto/ggcyto_par_set.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ggcyto_par_set
> ### Title: Set some default parameters for ggcyto
> ### Aliases: ggcyto_par_set
>
> ### ** Examples
>
> library(ggcyto)
> dataDir <- system.file("extdata",package="flowWorkspaceData")
> gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
loading R object...
loading tree object...
Done
>
> p <- ggcyto(gs, aes(x = CD4, y = CD8), subset = "CD3+")
> # 2d plot
> p <- p + geom_hex(bins = 64)
> p
Warning message:
Removed 4 rows containing missing values (geom_hex).
>
> #use instrument range by overwritting the default limits settings
> p + ggcyto_par_set(limits = "instrument")
Warning messages:
1: Removed 12952 rows containing non-finite values (stat_binhex).
2: Removed 25 rows containing missing values (geom_hex).
>
> #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)
Warning messages:
1: Removed 14972 rows containing non-finite values (stat_binhex).
2: Removed 48 rows containing missing values (geom_hex).
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
