cytof_clusterPlot: Scatter plot of the cluster results
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

cytof_clusterPlot

R Documentation

Scatter plot of the cluster results

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"
p = cytof_clusterPlot(data, xlab="dim1", ylab="dim2", cluster="cluster", sample = "sample")

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