plotVIP

plotVIP,ConsensusOPLS-method

Plot of VIP versus variable loadings in the optimal model.

Merging data from multiple sources is a relevant approach for
comprehensively evaluating complex systems. However, the inherent problems
encountered when analyzing single tables are amplified with the generation
of multi-block datasets, and finding the relationships between data layers
of increasing complexity constitutes a challenging task. For that purpose,
a generic methodology is proposed by combining the strength of established
data analysis strategies, i.e. multi-block approaches and the Orthogonal
Partial Least Squares (OPLS) framework to provide an efficient tool for the
fusion of data obtained from multiple sources. The package enables quick
and efficient implementation of the consensus OPLS model for any horizontal
multi-block data structures (observation-based matching). Moreover, it
offers an interesting range of metrics and graphics to help to determine
the optimal number of components and check the validity of the model
through permutation tests. Interpretation tools include score and loading
plots, Variable Importance in Projection (VIP), functionality predict for
SHAP computing, and performance coefficients such as R2, Q2, and DQ2
coefficients.
J. Boccard and D.N. Rutledge (2013) <doi:10.1016/j.aca.2013.01.022>.

Van T. Tran

ConsensusOPLS

Consensus OPLS for Multi-Block Data Fusion

Celine Bougel

Julien Boccard

Florence Mehl

Marie Tremblay-Franco

Mark Ibberson

Van Du T. Tran

plotVIP function

<dl><dt>object</dt>
<dd>An object of class <code>ConsensusOPLS</code>.</dd>
<dt>comp1</dt>
<dd>Latent variable for loadings on Y-axis. Default, the first
predictive component, <code>p_1</code>.</dd>
<dt>comp2</dt>
<dd>Latent variable for VIPs on X-axis. Default, the predictive
component, <code>p</code>.</dd>
<dt>blockId</dt>
<dd>The positions or names of the blocks for the plot.
Default, NULL, all.</dd>
<dt>col</dt>
<dd>A vector of color codes or names, one for each block. Default,
NULL, 2 to <code>length(blockId)+1</code>.</dd>
<dt>pch</dt>
<dd>A vector of graphic symbols, one for each block. Default, NULL,
1 to <code>length(blockId)</code>.</dd>
<dt>xlab</dt>
<dd>X-axis label. Default, NULL, Loading on <code>comp</code>.</dd>
<dt>ylab</dt>
<dd>Y-axis label. Default, NULL, VIP on <code>comp</code>.</dd>
<dt>...</dt>
<dd><code>plot</code> arguments.</dd></dl>

Arguments

VIP plot — plotVIP

<dl>

<dt>object</dt>
<dd>An object of class <code>ConsensusOPLS</code>.</dd>


<dt>comp1</dt>
<dd>Latent variable for loadings on Y-axis. Default, the first
predictive component, <code>p_1</code>.</dd>


<dt>comp2</dt>
<dd>Latent variable for VIPs on X-axis. Default, the predictive
component, <code>p</code>.</dd>


<dt>blockId</dt>
<dd>The positions or names of the blocks for the plot.
Default, NULL, all.</dd>


<dt>col</dt>
<dd>A vector of color codes or names, one for each block. Default,
NULL, 2 to <code>length(blockId)+1</code>.</dd>


<dt>pch</dt>
<dd>A vector of graphic symbols, one for each block. Default, NULL,
1 to <code>length(blockId)</code>.</dd>


<dt>xlab</dt>
<dd>X-axis label. Default, NULL, Loading on <code>comp</code>.</dd>


<dt>ylab</dt>
<dd>Y-axis label. Default, NULL, VIP on <code>comp</code>.</dd>


<dt>...</dt>
<dd><code>plot</code> arguments.</dd>

</dl>

plotVIP: VIP plot

Description

Usage

Value

Arguments