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Last data update: 2014.03.03

R: Popluation statistics layer

geom_stats

R Documentation

Popluation statistics layer

Description

It is a virtual layer and will be instanatiated as geom_label layer within ggycto.+ operator.

Usage

geom_stats(gate = NULL, ..., value = NULL, type = "percent",
  data_range = NULL, adjust = 0.5, label.padding = unit(0.05, "lines"),
  label.size = 0)

Arguments

`gate`	a 'filterList' or character (represent as a population node in GatingSet) if not supplied, ggcyto then tries to parse the gate from the first geom_gate layer.
`...`	other arguments passed to geom_label layer
`value`	the pre-calculated stats value. when supplied, the stats computing is skipped.
`type`	can be "percent", "count" or "MFI".
`data_range`	the data range for each channels
`adjust`	adjust the position of the centroid. from 0 to 1.
`label.padding,label.size`	arguments passed to geom_label layer

Details

So it is dedicated for ggcyto context and thus can't not be added to ggplot object directly.

Value

a geom_popStats layer

Examples

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+") + geom_hex(bins = 64)
p
# add gate and stats layer
p + geom_gate("CD4") + geom_stats()

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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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/geom_stats.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geom_stats
> ### Title: Popluation statistics layer
> ### Aliases: geom_stats
> 
> ### ** Examples
> 
> 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+") + geom_hex(bins = 64)
> p
Warning message:
Removed 4 rows containing missing values (geom_hex). 
> # add gate and stats layer
> p + geom_gate("CD4") + geom_stats()
Warning message:
Removed 4 rows containing missing values (geom_hex). 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>