PlotIndexesClust: Graphic visualization of an index

In ctsGE: Clustering of Time Series Gene Expression data

Description

The function generates graphs and tables of a specific index and its clusters. The user decides whether to supply the k or let the function calculate the k for the selected index

Usage

PlotIndexesClust(x, idx, k = NULL, scaling = TRUE)

Arguments

x	list of expression data and their indexes after running PreparingTheIndexes
idx	A character, the index to plot (e.g., for 8 time points "11100-1-1-1")
k	A numeric, number of clusters. If not given the function will calculate what is the optimal k for the index.
scaling	A boolean, default to TRUE, does the data should be standardized before clustered with K-means.

Value

A list with two objects:

1. Table of of a specific index and its clusters

2. Gene expression pattern graphs for each one of the clusters

See Also

ggplot, kmeans, ClustIndexes

Examples

data_dir <- system.file("extdata", package = "ctsGE")
files <- dir(path=data_dir,pattern = "\\.xls$")
rts <- readTSGE(files, path = data_dir,
labels = c("0h","6h","12h","24h","48h","72h"), skip = 10625 )
prts <- PreparingTheIndexes(rts)
pp <- PlotIndexesClust(prts,idx="00101-1")
pp$graphs # plots the line graphs

ctsGE documentation built on Nov. 8, 2020, 11:06 p.m.