Nothing
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width=8,
fig.height=6,
fig.retina=1
)
## ------------------------------------------------------------------------
library(cytofan)
## ----include=FALSE,echo=FALSE--------------------------------------------
library(bodenmiller)
library(ggplot2)
library(dplyr)
library(reshape2)
## ------------------------------------------------------------------------
data('refPhenoMat')
data('refFuncMat')
data('refAnnots')
refFullFrame <- melt(cbind(refPhenoMat,
refFuncMat))
names(refFullFrame) <- c('cell_id','Channel','value')
refFullFrame$Channel <- factor(refFullFrame$Channel,
levels=c(colnames(refPhenoMat),
colnames(refFuncMat)))
refFullFrame$Cells <- rep(refAnnots$Cells,
ncol(refPhenoMat)+ncol(refFuncMat))
## ------------------------------------------------------------------------
refFullFrame %>%
filter(Cells=='cd4+') %>%
ggplot(aes(x=Channel,y=value))+
geom_fan()+
facet_grid(.~Cells)+
theme(axis.text.x = element_text(angle = 45, hjust = 1))
## ------------------------------------------------------------------------
refFullFrame %>%
filter(Cells %in% c('cd4+','cd8+')) %>%
ggplot(aes(x=Channel,y=value))+
geom_fan()+
facet_grid(Cells~.)+
theme(axis.text.x = element_text(angle = 45, hjust = 1))
## ------------------------------------------------------------------------
data('untreatedPhenoMat')
data('untreatedFuncMat')
data('untreatedAnnots')
untreatedFullFrame <- melt(cbind(untreatedPhenoMat,
untreatedFuncMat))
names(untreatedFullFrame) <- c('cell_id','Channel','value')
untreatedFullFrame$Channel <- factor(untreatedFullFrame$Channel,
levels=c(colnames(untreatedPhenoMat),
colnames(untreatedFuncMat)))
untreatedFullFrame$Cells <- rep(untreatedAnnots$Cells,
ncol(untreatedPhenoMat)+ncol(untreatedFuncMat))
untreatedFullFrame$Treatment <- rep(untreatedAnnots$Treatment,
ncol(untreatedPhenoMat)+ncol(untreatedFuncMat))
## ------------------------------------------------------------------------
untreatedFullFrame %>%
filter(Cells=='cd4+') %>%
ggplot(aes(x=Channel,y=value))+
geom_fan()+
facet_grid(Treatment~Cells)+
theme(axis.text.x = element_text(angle = 45, hjust = 1))
## ----fig.width=12--------------------------------------------------------
untreatedFullFrame %>%
filter(Cells %in% c('cd4+','cd8+')) %>%
ggplot(aes(x=Channel,y=value))+
geom_fan()+
facet_grid(Cells~Treatment)+
theme(axis.text.x = element_text(angle = 45, hjust = 1))
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