amap: Heatmap and dendrogram from associations between all pairs of...

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/amap.R

Description

Clusters variables in a datafrome using dist = 1-A and plots a heatmap with cluster dendrogram attached.

Usage

1
amap(dataSet, palette, corAdjusted, method, title, ...)

Arguments

dataSet

the n x m data frame representing n samples of the m variables.

palette

colour palette to use for the heatmap.

corAdjusted

a flag which if set causes bi-variate A scores to be mutiplied by the sign of the same bi-variate correlation. This gives a direction to the association. defaults to FALSE.

method

the method to use for correlation association as performed by cor, one of "pearson", "spearman", "kendall". The default is "spearman".

title

a main title for the heatmap plot.

...

passed on to graphics routines ...

Details

uses heatmap.2 from the gplots package to display a heatmap and associated dendorgram with bi-variate scores provided by matie's A value. If required these scores can be expanded into the range [-1,1] through multiplication by the sign of the corresponding bi-variate correlation score.

Value

Returns nothing.

Note

The data set can be of any dimension.

Author(s)

Ben Murrell, Dan Murrell & Hugh Murrell.

References

This code was adapted from Moignard et al.

See Also

ma tap

Examples

1
2

Example output

[1] "Processing 11 variables. 55 pairs"
[1] "1 variable(s) complete"
[1] "2 variable(s) complete"
[1] "3 variable(s) complete"
[1] "4 variable(s) complete"
[1] "5 variable(s) complete"
[1] "6 variable(s) complete"
[1] "7 variable(s) complete"
[1] "8 variable(s) complete"
[1] "9 variable(s) complete"
[1] "10 variable(s) complete"

matie documentation built on May 29, 2017, 5:29 p.m.