plotSpatialPropAll

Color spots on the spatial coordinates plot according to their predicted cell
type proportions. All cell types are represented together using the same
color scale from 0 to 1.

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

plotSpatialPropAll 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>colors</dt>
<dd>Color scale to be used. It can be <code>"blues"</code> or
<code>"spectral"</code> (the former by default).</dd>
<dt>set</dt>
<dd>If results were simplified (see <code>?deconvSpatialDDLS</code>
for details), which results to plot (<code>raw</code> by default).</dd>
<dt>prediction</dt>
<dd>It can be <code>"Regularized"</code>, <code>"Intrinsic"</code> or
<code>"Extrinsic"</code> (<code>"Regularized"</code> by default).</dd>
<dt>size.point</dt>
<dd>Size of points (0.1 by default).</dd>
<dt>title</dt>
<dd>Title of plot.</dd>
<dt>nrow</dt>
<dd>Number of rows in the split plot.</dd>
<dt>ncol</dt>
<dd>Number of columns in the split plot.</dd>
<dt>theme</dt>
<dd>ggplot2 theme.</dd></dl>

Arguments

Plot predicted proportions for all cell types using spatial coordinates of
spots — plotSpatialPropAll

<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>colors</dt>
<dd>Color scale to be used. It can be <code>"blues"</code> or
<code>"spectral"</code> (the former by default).</dd>


<dt>set</dt>
<dd>If results were simplified (see <code>?deconvSpatialDDLS</code>
for details), which results to plot (<code>raw</code> by default).</dd>


<dt>prediction</dt>
<dd>It can be <code>"Regularized"</code>, <code>"Intrinsic"</code> or
<code>"Extrinsic"</code> (<code>"Regularized"</code> by default).</dd>


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


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


<dt>nrow</dt>
<dd>Number of rows in the split plot.</dd>


<dt>ncol</dt>
<dd>Number of columns in the split plot.</dd>


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

</dl>

plotSpatialPropAll: Plot predicted proportions for all cell types using spatial coordinates of spots

Description

Usage

Value

Arguments

See Also