plot_multi_module_enr

Generate gene set x ct_module heatmap showing co-expression module gene set enrichment results

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_multi_module_enr 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>ctypes</dt>
<dd>character A vector of cell type names corresponding to the module
numbers in mod_select, specifying the modules to compute enrichment for</dd>
<dt>modules</dt>
<dd>numeric A vector of module numbers corresponding to the cell
types in ctype, specifying the modules to compute enrichment for</dd>
<dt>sig_thresh</dt>
<dd>numeric P-value threshold for results to include. Only shows
a given gene set if at least one module has a result lower than the threshold.
(default=0.05)</dd>
<dt>db_use</dt>
<dd>character The database of gene sets to use. Database
options include "GO", "Reactome", "KEGG", "BioCarta", "Hallmark", "TF", and
"immuno". More than one database can be used. (default="GO")</dd>
<dt>max_plt_pval</dt>
<dd>max pvalue shown on plot, but not used to remove rows like
sig_thresh (default=.1)</dd>
<dt>h_w</dt>
<dd>numeric Vector specifying height and width (defualt=NULL)</dd></dl>

Arguments

Generate gene set x ct_module heatmap showing co-expression module gene set enrichment results — plot_multi_module_enr

<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>ctypes</dt>
<dd>character A vector of cell type names corresponding to the module
numbers in mod_select, specifying the modules to compute enrichment for</dd>


<dt>modules</dt>
<dd>numeric A vector of module numbers corresponding to the cell
types in ctype, specifying the modules to compute enrichment for</dd>


<dt>sig_thresh</dt>
<dd>numeric P-value threshold for results to include. Only shows
a given gene set if at least one module has a result lower than the threshold.
(default=0.05)</dd>


<dt>db_use</dt>
<dd>character The database of gene sets to use. Database
options include "GO", "Reactome", "KEGG", "BioCarta", "Hallmark", "TF", and
"immuno". More than one database can be used. (default="GO")</dd>


<dt>max_plt_pval</dt>
<dd>max pvalue shown on plot, but not used to remove rows like
sig_thresh (default=.1)</dd>


<dt>h_w</dt>
<dd>numeric Vector specifying height and width (defualt=NULL)</dd>

</dl>

plot_multi_module_enr: Generate gene set x ct_module heatmap showing co-expression module gene set enrichment results

Description

Usage

Value

Arguments