cytof_clusterPlot: Scatter plot of the cluster results

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

Description

Dot plot visualization of the cluster results, with color indicating different clusters, and shape of different samples.

Usage

cytof_clusterPlot(data, xlab, ylab, cluster, sample, title = "cluster",
  type = 1, point_size = NULL, addLabel = TRUE, labelSize = 10,
  sampleLabel = TRUE, labelRepel = FALSE, fixCoord = TRUE, clusterColor)

Arguments

data	The data frame of cluster results, which should contains at least xlab, ylab and cluster.
xlab	The column name of the x axis in input data.
ylab	The column name of the y axis in input data.
cluster	The column name of cluster in input data.
sample	The column name of the sample in input data.
title	The title of the plot.
type	Plot type, 1 indicates combined plot, 2 indicated grid facet plot seperated by samples.
point_size	Size of the dot.
addLabel	If TRUE, add cluster labels.
labelSize	Size of cluster labels.
sampleLabel	If TRUE, use point shapes to represent different samples.
labelRepel	If TRUE, repel the cluste labels to avoid label overlapping.
fixCoord	If TRUE, fix the Cartesian coordinates.
clusterColor	Manually specify the colour of each cluster (mainly for ShinyAPP usage).

Value

The ggplot object of the scatter cluster plot.

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 <- c(rep(1,100), rep(2,100), rep(3,100))
rnames <- paste(paste('sample_', c('A','B','C'), sep = ''), rep(1:100,each = 3), sep='_') 
data <- data.frame(dim1 = x, dim2 = y, cluster = c)
rownames(data) <- rnames
data$sample <- "data"
cytof_clusterPlot(data, xlab="dim1", ylab="dim2", cluster="cluster", sample = "sample")

JinmiaoChenLab/cytofkit documentation built on Dec. 20, 2020, 8:52 p.m.