Plot Fan Plots for Cytometry Data using 'ggplot2'.

cytofan

cytofan implements the concept of fan plots (Britton, E.; Fisher, P. & J. Whitley (1998) The Inflation Report Projections: Understanding the Fan Chart) for cytometry data in ggplot2.

The cytofan package was implemented following up on a gist written shortly after the fanplot package was released. Compared to ggfan, cytofan uses categorical data as input on the x axis.

Installation

You can install cytofan from github with:

# install.packages("devtools")
devtools::install_github("yannabraham/cytofan")

Example

cytofan can be used to visualize differences between populations identifed using mass cytometry:

library(cytofan)
#> Loading required package: ggplot2
library(bodenmiller)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(reshape2)

data("refPhenoMat")
data("refAnnots")

bind_cols(refAnnots,
          as.data.frame(refPhenoMat)) %>%
  melt(.,measure.vars=colnames(refPhenoMat),
       variable.name='Channel') %>%
  filter(Cells %in% c('cd4+','cd8+','igm+','igm-')) %>%
  ggplot(aes(x=Channel,y=value))+
  geom_fan()+
  facet_grid(Cells~.)