cytof_clusterPlot: Scatter plot of the cluster results

Description Usage Arguments Value Examples

View source: R/cytof_postProcess.R

Description

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

Usage

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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

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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")

cytofkit documentation built on Aug. 9, 2017, 2 a.m.