timeclustplot: Plot clustering results for time course data.

In TCseq: Time course sequencing data analysis

Description

This function plots the clusters generated from timeclust. For fuzzy cmeans clustering, data points are color-coded according to membership values, the color palettes can be customized.

Usage

timeclustplot(object = NULL, categories = "timepoint",
  value = "expression", cols = NULL, cl.color = "gray50",
  membership.color = rainbow(30, s = 3/4, v = 1, start = 1/6),
  title.size = 18, axis.line.size = 0.6, axis.title.size = 18,
  axis.text.size = 16, legend.title.size = 14, legend.text.size = 14)

Arguments

object	a TCA object or a clust object
categories	character string giving the x-axis label
value	character string giving the y-axis label
cols	integer value specifying number of columns in the final layout.
cl.color	character string specifying a color for hard clustering.
membership.color	color palettes, a character vector of n colors
title.size	numeric value specifying the font size of title of each plot in the layout
axis.line.size	numeric value specifying the size of both axis lines
axis.title.size	numeric value specifying the font size of titles of both axis
axis.text.size	numeric value specifying the font size of labels of both axis
legend.title.size	numeric value specifying the font size of legend title
legend.text.size	numeric value specifying the font size of legend text

Value

Plot all clusters in one plot and return a list of ggplot objects, each object is for one cluster. The ggplot object can be drawed by calling print.ggplot

Author(s)

Mengjun Wu

Examples

x <- matrix(sample(500, 1600, replace = TRUE), nrow = 200,
            dimnames = list(paste0('peak', 1:200), 1:8))
clust_res <- timeclust(x, algo = 'cm', k = 4, standardize = TRUE)
p <- timeclustplot(clust_res, cols =2)
# to plot a individual cluster
print (p[[2]]) # plot cluster 2
print (p[[3]]) # plot cluster 3

TCseq documentation built on Nov. 8, 2020, 5:46 p.m.