clusGPS-class: Class '"clusGPS"'

In chroGPS: chroGPS2: Generation, visualization and differential analysis of epigenome maps

Description

Agglomerative Nesting for a distGPS object. Contains probability contours and bayesian posterior probability of mis-classification for the clusters evaluated.

Details

Parameters for the S4 plot method for mds objects.

x:

Object of class "mds" with a 2D or 3D Multidimensional Scaling to be plotted.

drawlabels:

TRUE to use rownames of the MDS points as text labels.

labels:

Alternative character vector giving the text labels for the MDS points.

plantar:

If a 3D MDS is used, set plantar to TRUE to plot projected views of the MDS using XY, YZ and XZ axis decomposition.

point.cex:

Size of the points / spheres for the MDS plot.

text.cex:

Size of text labels for the MDS points.

text.pos:

Alignment position of the text labels respective to its points (1,2,3,4).

point.col:

Color for the MDS points / spheres.

text.col:

Color for the MDS text labels.

point.pch:

PCH type for the MDS points.

type.3d:

Use 'p' for points, 's' for spheres.

radius:

Radius for the spheres on a 3D MDS plot. Automatically generated from point.cex and the number of points in the MDS.

app:

Appearance of the 3D spheres on a 3D MDS plot, can be 'fill', 'lines', 'grid'.

alpha:

Number between 0 and 1 with the level of transparency to be used on spheres on a 3D MDS.

scalecol:

Set to TRUE to use a color scale for points, for instance to color points (genes) according to their expression level on a chroGPS-genes MDS plot.

scale:

Scale to use to generate scale colors (for instance normalized gene expression for each element (gene) on chroGPS-genes MDS).

palette:

Color palette to be used for scale colors.

Objects from the Class

Objects can be created by calls of the form new("clusGPS", ...).

Slots

h:

Object of class "hclust" with Agglomerative Nesting or user-provided cluster object.

clus:

Object of class "list" with probability contour and bayesian posterior probability of mis-classification information for the clusters evaluated.

adjusted:

Object of class "logical" indicating if bayesian posterior probabilities of mis-classification are adjusted for multiple testing.

Author(s)

Oscar Reina

Examples

showClass("clusGPS")

chroGPS documentation built on Oct. 31, 2019, 4:52 a.m.