ggflow: Draw a FlowJo-style (sort of) Plot Using ggplot Semantics

In rogerswt/wadeTools: Wade's Hodgepodge of Flow Cytometry Functions

Draw a FlowJo-style (sort of) Plot Using ggplot Semantics

Description

Draw a picture, with default colors reminiscent of FlowJo.

ggflow uses ggplot semantics to render bivariate flow cytometry plots. If called "bare", it draws a picture. If its return value is captured in a variable, further manipulation of the plot is possible. See the examples below.

Usage

ggflow(
  ff,
  params = c("FSC-A", "SSC-A"),
  colors = c("flowjo", "viridis", "plasma", "magma"),
  resolution = c("medium", "very_coarse", "coarse", "fine"),
  trans_sc = c("linear", "biexp", "asinh", "log"),
  trans_fl = c("biexp", "asinh", "log", "linear"),
  a = 0.002,
  cofactor = 5,
  indicate_zero = TRUE,
  xlim = NULL,
  ylim = NULL
)

Arguments

ff	The flowFrame to be plotted
params	A vector of length 2 indicating the parameters of ff to be plotted
colors	A color palette for rendering densities of events. Currently, one of c("flowjo", "viridis", "plasma", "magma"). Can be abbreviated.
resolution	One of c("medium", "coarse", "fine"). Can be abbreviated.
trans_sc	The transformation that was applied to the scattering parameters of ff. Currently, one of c("linear", "biexp", "asinh", "log").
trans_fl	The transformation that was applied to the fluorescence parameters of ff. Currently, one of c("linear", "biexp", "asinh", "log").
a	Adjustable parameter "a" for the biexp transformation. Default = 0.002.
cofactor	Adjustable parameter "cofactor" for asinh transformation. Default = 5.
indicate_zero	Boolean, should we indicate the location of 0?
xlim	The limits of the plot in the x direction. NULL will apply sensible defaults.
ylim	The limits of the plot in the y direction. NULL will apply sensible defaults.

Value

A ggplot object.

Examples

# get some example data
filename = system.file("extdata", "example1.fcs", package = "wadeTools")
ff = get_sample(filename)
# Recall that get_sample by default applies linear transformation to scattering
# parameters and biexponential transformation to fluorescence parameters.

# Plot ff on default FSC-A, SSC-A dimensions (notice linear axes)
ggflow(ff)

# another plot of fluorescence parameters.  Note the biexponential axes.
ggflow(ff, c("CD4PETR", "CD8Q705"))

# one fluorescence (biexp) versus one scattering (linear)
ggflow(ff, c("SSC-A", "CD3Q605"))

# Add a title
ggflow(ff, c("CD4PETR", "CD8Q705")) + labs(title = "Title of Plot")

# or if you prefer,
p = ggflow(ff, c("CD4PETR", "CD8Q705"))
p + labs(title = "Another plot with a title")

# Check out the other color schemes
library("gridExtra")
p1 = ggflow(ff, c("CD3Q605", "LIVEDEAD")) + labs(title = "flowjo") + theme(legend.position = 'right')
p2 = ggflow(ff, c("CD3Q605", "LIVEDEAD"), colors = "v") + labs(title = "viridis") + theme(legend.position = 'right')
p3 = ggflow(ff, c("CD3Q605", "LIVEDEAD"), colors = "m") + labs(title = "magma") + theme(legend.position = 'right')
p4 = ggflow(ff, c("CD3Q605", "LIVEDEAD"), colors = "p") + labs(title = "plasma") + theme(legend.position = 'right')
p = grid.arrange(p1, p2, p3, p4, nrow = 2, ncol = 2)
p

# Override plot limits and default resolution
ggflow(ff, c("CD45RAQ655","CD11BAPCCY7"), xlim = bx(c(-1e3,1e6)), ylim = bx(c(-1e3,1e6)), res = 'f')

# make a plot and add some blob boundaries
params = c("SSC-A", "CD3Q605")
x_range = 0.5
p1 = ggflow(ff, params)
bb1 = blob.boundary(ff, c("SSC-A", "CD3Q605"), x_range = c(x_range, Inf), location = c(1.5, bx(8000)), height = .25)
b1 = geom_path(bb1, mapping = aes(x = `SSC-A`, y = CD3Q605, group = 1))
bb2 = blob.boundary(ff, c("SSC-A", "CD3Q605"), x_range = c(x_range, Inf), location = c(3, bx(500)), height = .25)
b2 = geom_path(bb2, mapping = aes(x = `SSC-A`, y = CD3Q605, group = 1))
bb3 = blob.boundary(ff, c("SSC-A", "CD3Q605"), x_range = c(x_range, Inf), location = c(0, 0), height = .25)
b3 = geom_path(bb3, mapping = aes(x = `SSC-A`, y = CD3Q605, group = 1))
vline = geom_vline(aes(xintercept = x_range), linetype = "dotted")
p1 + b1 + b2 + b3 + vline

rogerswt/wadeTools documentation built on Feb. 16, 2023, 7:47 a.m.