cytof_colorPlot: Plot the data with color-coded marker values

In JinmiaoChenLab/cytofkit2: cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets

Plot the data with color-coded marker values

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")

JinmiaoChenLab/cytofkit2 documentation built on May 12, 2022, 8:09 a.m.