plot_mod_and_lig

Plot trio of associations between ligand expression, module eigengenes, and
factor scores

Single-cell Interpretable Tensor Decomposition (scITD) employs the
Tucker tensor decomposition to extract multicell-type gene expression patterns
that vary across donors/individuals. This tool is geared for use with single-cell
RNA-sequencing datasets consisting of many source donors. The method has a wide
range of potential applications, including the study of inter-individual variation
at the population-level, patient sub-grouping/stratification, and the analysis
of sample-level batch effects. Each "multicellular process" that is extracted
consists of (A) a multi cell type gene loadings matrix and (B) a
corresponding donor scores vector indicating the level at which the corresponding
loadings matrix is expressed in each donor. Additional methods are implemented
to aid in selecting an appropriate number of factors and to evaluate stability
of the decomposition. Additional tools are provided for downstream analysis,
including integration of gene set enrichment analysis and ligand-receptor analysis.
Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Jonathan Mitchel

scITD

Single-Cell Interpretable Tensor Decomposition

Evan Biederstedt

Peter Kharchenko

plot_mod_and_lig function

<dl><dt>container</dt>
<dd>environment Project container that stores sub-containers
for each cell type as well as results and plots from all analyses</dd>
<dt>factor_select</dt>
<dd>numeric The factor to use</dd>
<dt>mod_ct</dt>
<dd>character The name of the cell type for the corresponding module</dd>
<dt>mod</dt>
<dd>numeric The number of the corresponding module</dd>
<dt>lig_ct</dt>
<dd>character The name of the cell type where the ligand is expressed</dd>
<dt>lig</dt>
<dd>character The name of the ligand to use</dd></dl>

Arguments

Plot trio of associations between ligand expression, module eigengenes, and
factor scores — plot_mod_and_lig

<dl>

<dt>container</dt>
<dd>environment Project container that stores sub-containers
for each cell type as well as results and plots from all analyses</dd>


<dt>factor_select</dt>
<dd>numeric The factor to use</dd>


<dt>mod_ct</dt>
<dd>character The name of the cell type for the corresponding module</dd>


<dt>mod</dt>
<dd>numeric The number of the corresponding module</dd>


<dt>lig_ct</dt>
<dd>character The name of the cell type where the ligand is expressed</dd>


<dt>lig</dt>
<dd>character The name of the ligand to use</dd>

</dl>

plot_mod_and_lig: Plot trio of associations between ligand expression, module eigengenes, and factor scores

Description

Usage

Value

Arguments