peakCMeans {geneExpression} R Documentation

clustering analysis of time course data

Description

<br /> 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,
    margin = "padding:100px 100px 300px 100px;",
    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;",
    grid.fill = "LightGray",
    grid.draw = TRUE,
    x.lab.rotate = 45);

Arguments

matrix

[as Matrix]

nsize

threshold

[as double]

plotSize

colorSet

[as string]

fuzzification

[as double]

memberCutoff

[as double]

empty.shared

how many clusters will be assigned to a gene feature when there is no cluster that its membership value is greater than the memberCutoff. [as integer]

max.cluster.shared

[as integer]

xlab

[as string]

ylab

[as string]

top.members

[as double]

margin

cluster.label.css

[as string]

legend.title.css

[as string]

legend.tick.css

[as string]

axis.tick.css

[as string]

axis.label.css

[as string]

grid.fill

[as string]

grid.draw

[as boolean]

x.lab.rotate

[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 vector of the EntityClusterModel data that contains the object cluster patterns

  2. 'image' is a bitmap image that plot based on the object cluster patterns data.

  3. 'pdf' is a pdf image that could be edit

  4. 'cmeans' is the raw ExpressionPattern object of the cmeans clustering result

NULL will be returns if the given expression matrix is empty.

clr value class

Examples

[Package geneExpression version 1.0.0.0 Index]