ggcyto_add {ggcyto} | R Documentation

## overloaded '+' method for ggcyto

### Description

It tries to copy pData from ggcyto object to the gate layers so that the gate layer does not need to have 'pd' to be supplied explicitly by users. It also calculates population statistics when geom_stats layer is added. It supports addition ggcyto layers such as 'ggcyto_par' and 'labs_cyto'.

### Usage

    e1 + e2

### Arguments

`e1` | An object of class `ggcyto` or a class inheriting from `ggcyto`, such as `ggcyto_flowSet`, `ggcyto_GatingSet`, or `ggcyto_GatingLayout`. In the case of `ggcyto_GatingLayout`, the component of `e2` will be added to each subsidiary plot.
`e2` | A component to add to `e1`

### Value

ggcyto object

### Examples

    ## flowSet
    data(GvHD)
    fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]]
    p <- ggcyto(fs, aes(x = `FSC-H`, y =  `SSC-H`)) + geom_hex(bins = 128)
    #add rectangleGate layer (2d)
    rect.g <- rectangleGate(list("FSC-H" =  c(300,500), "SSC-H" = c(50,200)))
    rect.gates <- sapply(sampleNames(fs), function(sn)rect.g)
    p + geom_gate(rect.gates) + geom_stats()

    ## GatingSet
    dataDir <- system.file("extdata",package="flowWorkspaceData")
    gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
    p <- ggcyto(gs, aes(x = CD4, y = CD8), subset = "CD3+") + geom_hex(bins = 64)
    p <- p + geom_gate("CD4") + geom_stats() #plot CD4 gate and it is stats
    p
    p + axis_x_inverse_trans() #inverse transform the x axis into raw scale

    ## GatingLayout
    #autplot for GatingSet
    dataDir <- system.file("extdata",package="flowWorkspaceData")
    gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
    gh <- gs[[1]]
    p <- autoplot(gh)
    class(p)
    # customize the font size of strip text for each ggcyo plots contained in GatingLayout object
    p + theme(strip.text = element_text(size = 14))

[Package ggcyto version 1.15.2 Index]