timeclustplot {TCseq} | R Documentation |
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.
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)
object |
a |
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 |
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
Mengjun Wu
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