## ---- echo=FALSE---------------------------------------------------------
knitr::opts_chunk$set(message = FALSE, warning = FALSE)

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library(ggcyto)
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]]
fr <- fs[[1]]

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p <- ggcyto(fs, aes(x = `FSC-H`)) 
class(p)
is(p, "ggplot")

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p1 <- p + geom_histogram() 
p1

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pData(fs)
p1 + facet_grid(Patient~Visit)

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p + geom_density()

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p + geom_density(fill = "black")

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ggcyto(fs, aes(x = `FSC-H`, fill = name)) + geom_density(alpha = 0.2)

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ggplot(fs, aes(x = `FSC-H`, fill = name)) + geom_density(alpha = 0.2)

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# 2d hex
p <- ggcyto(fs, aes(x = `FSC-H`, y =  `SSC-H`))
p <- p + geom_hex(bins = 128)
p

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p <- p + ylim(c(10,9e2)) + xlim(c(10,9e2))   
p

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p + scale_fill_gradientn(colours = rainbow(7), trans = "sqrt")

p + scale_fill_gradient(trans = "sqrt", low = "gray", high = "black")


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# estimate a lymphGate
lg <- flowStats::lymphGate(fr, channels=c("FSC-H", "SSC-H"),scale=0.6)
norm.filter <- lg$n2gate
#fit norm2 filter to multiple samples
fres <- filter(fs, norm.filter)
#extract the polygonGate for each sample
poly.gates <- lapply(fres, function(res)flowViz:::norm2Polygon(filterDetails(res, "defaultLymphGate")))
poly.gates

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p + geom_gate(poly.gates)

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rect.g <- rectangleGate(list("FSC-H" =  c(300,500), "SSC-H" = c(50,200)))
rect.gates <- sapply(sampleNames(fs), function(sn)rect.g)

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p + geom_gate(rect.gates)

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p + geom_gate(rect.gates) + geom_stats(size = 3)

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den.gates.x <- fsApply(fs, openCyto::gate_mindensity, channel = "FSC-H", gate_range = c(100, 300), adjust = 1)
p + geom_gate(den.gates.x) + geom_stats()

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den.gates.y <- fsApply(fs, openCyto::gate_mindensity, channel = "SSC-H", gate_range = c(100, 500), adjust = 1, positive = FALSE)

p + geom_gate(den.gates.y) + geom_stats(value = lapply(rect.gates, function(g)0.1))

## ------------------------------------------------------------------------
ggcyto(fs, aes(x = `FSC-H`)) + geom_density(fill = "black", aes(y = ..scaled..)) + geom_gate(den.gates.x)  + geom_stats(type = "count")

## ------------------------------------------------------------------------
p + geom_gate(poly.gates) + geom_gate(rect.gates) + geom_stats(size = 3)

## ------------------------------------------------------------------------
p + geom_gate(poly.gates) + geom_gate(rect.gates) + geom_stats(gate = poly.gates, size = 3)

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class(p)
class(p$data)

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p <- as.ggplot(p)

class(p)
class(p$data)