plotSpatialClustering

Color spots on the spatial coordinates according to the results of
clustering based on predicted proportions.

Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.

Diego Ma<c3><b1>anes

SpatialDDLS

Deconvolution of Spatial Transcriptomics Data Based on Neural
Networks

Diego Mañanes

Carlos Torroja

Fatima Sanchez-Cabo

plotSpatialClustering function

<dl><dt>object</dt>
<dd>A <code>SpatialDDLS</code> object.</dd>
<dt>index.st</dt>
<dd>Index of the spatial transcriptomics data to be plotted. It
can be either a position or a name if a named list of
<code>SpatialExperiment</code> objects was provided.</dd>
<dt>method</dt>
<dd>Clustering method results to plot. It can be <code>"graph"</code> or
<code>"k.means"</code>. If missing, the first configuration found in the object
will be plotted.</dd>
<dt>k.nn</dt>
<dd>Number of nearest neighbors used if <code> method == "graph"</code>.</dd>
<dt>k.centers</dt>
<dd>Number of k centers used if <code> method == "k.means"</code>.</dd>
<dt>colors</dt>
<dd>Vector of colors to be used.</dd>
<dt>size.point</dt>
<dd>Size of points (0.1 by default).</dd>
<dt>title</dt>
<dd>Title of plot.</dd>
<dt>theme</dt>
<dd>ggplot2 theme.</dd></dl>

Arguments

Plot results of clustering based on predicted cell proportions — plotSpatialClustering

<dl>

<dt>object</dt>
<dd>A <code>SpatialDDLS</code> object.</dd>


<dt>index.st</dt>
<dd>Index of the spatial transcriptomics data to be plotted. It
can be either a position or a name if a named list of
<code>SpatialExperiment</code> objects was provided.</dd>


<dt>method</dt>
<dd>Clustering method results to plot. It can be <code>"graph"</code> or
<code>"k.means"</code>. If missing, the first configuration found in the object
will be plotted.</dd>


<dt>k.nn</dt>
<dd>Number of nearest neighbors used if <code> method == "graph"</code>.</dd>


<dt>k.centers</dt>
<dd>Number of k centers used if <code> method == "k.means"</code>.</dd>


<dt>colors</dt>
<dd>Vector of colors to be used.</dd>


<dt>size.point</dt>
<dd>Size of points (0.1 by default).</dd>


<dt>title</dt>
<dd>Title of plot.</dd>


<dt>theme</dt>
<dd>ggplot2 theme.</dd>

</dl>

plotSpatialClustering: Plot results of clustering based on predicted cell proportions

Description

Usage

Value

Arguments

See Also