peakCMeans {geneExpression} R Documentation

clustering analysis of time course data

Description


This function performs clustering analysis of time course data

Usage

peakCMeans(matrix,
    nsize = "3,3",
    threshold = 10,
    fuzzification = 2,
    plotSize = "8100,5200",
    colorSet = "Jet",
    memberCutoff = 0.8,
    empty.shared = 2,
    max.cluster.shared = 3,
    xlab = "Spatial Regions",
    ylab = "z-score(Normalized Intensity)",
    top.members = 0.2,
    cluster.label.css = "font-style: normal; font-size: 20; font-family: Bookman Old Style;",
    legend.title.css = "font-style: normal; font-size: 10; font-family: Microsoft YaHei;",
    legend.tick.css = "font-style: normal; font-size: 10; font-family: Microsoft YaHei;",
    axis.tick.css = "font-style: normal; font-size: 12; font-family: Segoe UI;",
    axis.label.css = "font-style: normal; font-size: 10; font-family: Microsoft YaHei;");

Arguments

matrix

A gene expression data matrix object. [as Matrix]

nsize

the layout of the cmeans clustering visualization. [as string]

threshold

the cmeans threshold. [as double]

plotSize

the image size of the cmeans plot

colorSet

the color palatte name. [as string]

fuzzification

cmeans fuzzification parameter. [as double]

memberCutoff

the cmeans membership cutoff value for create a molecule cluster. [as double]

env

[as Environment]

Details

Authors

phenotype_kit

Value

this function returns a tuple list that contains the pattern cluster matrix and the cmeans pattern plots. 1. 'pattern' is a dataframe object that contains the object cluster patterns 2. 'image' is a bitmap image that plot based on the object cluster patterns data.

clr value class

Examples

[Package geneExpression version 1.0.0.0 Index]