cytof_colorPlot: Plot the data with color-coded marker values

In cytofkit: cytofkit: an integrated mass cytometry data analysis pipeline

Description

Plot the data with color-coded marker values

Usage

cytof_colorPlot(data, xlab, ylab, zlab, colorPalette = c("bluered",
  "spectral1", "spectral2", "heat"), limits = c(quantile(data[, zlab], 0.02),
  quantile(data[, zlab], 0.98)), pointSize = 0.5, alpha = 1,
  removeOutlier = TRUE)

Arguments

data	A dataframe containing the xlab, ylab and zlab.
xlab	The column name of data for x lab.
ylab	The column name of data for y lab.
zlab	The column name of data for z lab.
colorPalette	Color Palette.
limits	Range for z lab, defaults to existing min, and max set at 98th percentile value.
pointSize	Size of the point.
alpha	Transparency of point. 1 is opaque, 0 is completely transparent.
removeOutlier	If TRUE, remove the outliers.

Value

A ggplot object.

Examples

x <- c(rnorm(100, mean = 1), rnorm(100, mean = 3), rnorm(100, mean = 9))
y <- c(rnorm(100, mean = 2), rnorm(100, mean = 8), rnorm(100, mean = 5))
c <- rnorm(300, 10, 5)
data <- data.frame(dim1 = x, dim2 = y, marker = c)
cytof_colorPlot(data = data, xlab = "dim1", ylab = "dim2", zlab = "marker")

Example output

Loading required package: ggplot2
Loading required package: plyr
Warning message:
no DISPLAY variable so Tk is not available 

cytofkit documentation built on Nov. 1, 2018, 3:50 a.m.