knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-" )
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.
You can install cytofan from github with:
# install.packages("devtools") devtools::install_github("yannabraham/cytofan")
cytofan
can be used to visualize differences between populations identifed using mass cytometry:
library(cytofan) library(bodenmiller) library(dplyr) 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~.)
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