vignettes/advanced/ggplot.flowSet.2d.Rmd
ggplot.flowSet.2d.Rmdggcyto makes ggplot2 to be able to work with Cytometry data, namely flowSet/ncdfFlowSet or flowFrame S4 objects.
library(ggcyto) data(GvHD) fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]] fr <- fs[[1]]
# 2d hex p <- ggplot(fr, aes(x = `FSC-H`, y = `SSC-H`)) p + stat_binhex()

# change the smooth color myColor <- rev(RColorBrewer::brewer.pal(11, "Spectral")) myColor_scale_fill <- scale_fill_gradientn(colours = myColor) p + myColor_scale_fill + stat_binhex()

#change the bins p + myColor_scale_fill + stat_binhex(bins = 64)

# sqr trans binned color myColor_scale_fill_sqrt <- scale_fill_gradientn(colours = myColor, trans = "sqrt") p1 <- p + myColor_scale_fill_sqrt + stat_binhex(bins = 64) p1


# add contour p <- p + myColor_scale_fill p + stat_binhex(bins = 64) + geom_density2d(colour = "black")

# non-binned dot plot df <- fortify(fr) cols <- densCols(df[,`FSC-H`], df[,`SSC-H`], colramp = flowViz::flowViz.par.get("argcolramp")) p1 <- ggplot(df, aes(x = `FSC-H`, y = `SSC-H`)) p1 + geom_point(color = cols)

# multiple samples p1 <- ggplot(mapping = aes(x = `FSC-H`, y = `SSC-H`)) + myColor_scale_fill + facet_grid(Patient~Visit) p1 + stat_binhex(data = fs, bins = 64)

# color scale is different when plotting single sample p1 + stat_binhex(data = fs[6], bins = 64)

# display density instead p1 + stat_binhex(data = fs[6], bins = 64, aes(fill = ..density..))

# the color scale difference is reduced p1 + stat_binhex(data = fs, bins = 64, aes(fill = ..density..))

# non-binned dot plot df <- fortify(fr) cols <- densCols(df[,`FSC-H`], df[,`SSC-H`], colramp = flowViz::flowViz.par.get("argcolramp")) p <- ggplot(df, aes(x = `FSC-H`, y = `SSC-H`)) p + geom_point(color = cols)
