plotSpatialProp

Color spots on the spatial coordinates according to the predicted proportions
of a particular cell type. Color scale is adapted depending on the range of
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

plotSpatialProp 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>cell.type</dt>
<dd>Cell type predicted proportions to color spots by.</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), what 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>limits</dt>
<dd>A vector of two elements indicating wanted limits for color
scale. If <code>NULL</code> (by default), color scale is adjusted to max and min
predicted proportions.</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 predicted proportions for a specific cell type using spatial coordinates
of spots — plotSpatialProp

<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>cell.type</dt>
<dd>Cell type predicted proportions to color spots by.</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), what 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>limits</dt>
<dd>A vector of two elements indicating wanted limits for color
scale. If <code>NULL</code> (by default), color scale is adjusted to max and min
predicted proportions.</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>

plotSpatialProp: Plot predicted proportions for a specific cell type using spatial coordinates of spots

Description

Usage

Value

Arguments

See Also