prepDataForggHeatmap

Converts a matrix to the correct format for heatmapping in 
``ggplot2`` with an option to order rows and columns.

Integrative clustering and semi-supervised prediction.
This package includes a 'C++' implementation of both semi-supervised and
unsupervised Multiple Dataset Integration (MDI; Kirk et al., 2012
<https://doi-org.ezp.lib.cam.ac.uk/10.1093/bioinformatics/bts595>), an
extension of Bayesian mixture models to the integrative (multiple dataset or
multi-modal) setting such as multi-omics analysis. The package also includes
Bayesian mixture models. Densities allowed within MDI and the mixture model
are Gaussian with full and diagonal covariance matrices, categorical, Gaussian
with a Gaussian process (GP) prior on the mean parameter. The GP model
implemented canonly handle data with common time points of equal separation.
The Gaussian and GP models can be augmented with a global multivariate t
distribution to handle outliers.

Stephen Coleman

mdir

Bayesian Model-Based Clustering of Multi-Modal Data

Paul Kirk

Chris Wallace

Oliver Crook

prepDataForggHeatmap function

<dl><dt>X</dt>
<dd>Matrix.</dd>
<dt>row_order</dt>
<dd>Order for rows to be represented in heatmap along the 
y-axis. Can be ``NULL`` (order defined on data using `hierarchical 
clustering), ``FALSE`` (no ordering applied), or a vector of indices.</dd>
<dt>col_order</dt>
<dd>Order for columns to be represented in heatmap along the 
x-axis. Can be ``NULL`` (order defined on data using `hierarchical 
clustering), ``FALSE`` (no ordering applied), or a vector of indices.</dd>
<dt>x_axis</dt>
<dd>The name for the column defining the x-axis. Defaults to 
``"Feature"``.</dd>
<dt>y_axis</dt>
<dd>The name for the column defining the y-axis. Defaults to 
``"Item"``.</dd></dl>

Arguments

Prepare data for ggplot heatmap — prepDataForggHeatmap

<dl>

<dt>X</dt>
<dd>Matrix.</dd>


<dt>row_order</dt>
<dd>Order for rows to be represented in heatmap along the 
y-axis. Can be ``NULL`` (order defined on data using `hierarchical 
clustering), ``FALSE`` (no ordering applied), or a vector of indices.</dd>


<dt>col_order</dt>
<dd>Order for columns to be represented in heatmap along the 
x-axis. Can be ``NULL`` (order defined on data using `hierarchical 
clustering), ``FALSE`` (no ordering applied), or a vector of indices.</dd>


<dt>x_axis</dt>
<dd>The name for the column defining the x-axis. Defaults to 
``"Feature"``.</dd>


<dt>y_axis</dt>
<dd>The name for the column defining the y-axis. Defaults to 
``"Item"``.</dd>

</dl>

prepDataForggHeatmap: Prepare data for ggplot heatmap

Description

Usage

Value

Arguments