plot_donor_props

Plot donor celltype/subtype proportions against each factor

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_donor_props function

<dl><dt>donor_props</dt>
<dd>data.frame Donor proportions as output from compute_donor_props()</dd>
<dt>donor_scores</dt>
<dd>data.frame Donor scores from tucker results</dd>
<dt>significance</dt>
<dd>numeric F-Statistics as output from compute_associations()</dd>
<dt>ctype_mapping</dt>
<dd>character The cell types corresponding with columns of donor_props (default=NULL)</dd>
<dt>stat_type</dt>
<dd>character Either "fstat" to get F-Statistics, "adj_rsq" to get adjusted
R-squared values, or "adj_pval" to get adjusted pvalues (default='adj_pval')</dd>
<dt>n_col</dt>
<dd>numeric The number of columns to organize the plots into (default=2)</dd></dl>

Arguments

Plot donor celltype/subtype proportions against each factor — plot_donor_props

<dl>

<dt>donor_props</dt>
<dd>data.frame Donor proportions as output from compute_donor_props()</dd>


<dt>donor_scores</dt>
<dd>data.frame Donor scores from tucker results</dd>


<dt>significance</dt>
<dd>numeric F-Statistics as output from compute_associations()</dd>


<dt>ctype_mapping</dt>
<dd>character The cell types corresponding with columns of donor_props (default=NULL)</dd>


<dt>stat_type</dt>
<dd>character Either "fstat" to get F-Statistics, "adj_rsq" to get adjusted
R-squared values, or "adj_pval" to get adjusted pvalues (default='adj_pval')</dd>


<dt>n_col</dt>
<dd>numeric The number of columns to organize the plots into (default=2)</dd>

</dl>

plot_donor_props: Plot donor celltype/subtype proportions against each factor

Description

Usage

Value

Arguments