plot_select_sets

Plot enrichment results for hand picked gene sets

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_select_sets 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>factors_all</dt>
<dd>numeric Vector of one or more factor numbers to get plots for</dd>
<dt>sets_plot</dt>
<dd>character Vector of gene set names to show enrichment values for</dd>
<dt>color_sets</dt>
<dd>named character Values are colors corresponding to each set,
with names as the gene set names (default=NULL)</dd>
<dt>cl_rows</dt>
<dd>logical Set to TRUE to cluster gene set results (default=FALSE)</dd>
<dt>h_w</dt>
<dd>numeric Vector specifying height and width (defualt=NULL)</dd>
<dt>myfontsize</dt>
<dd>numeric Gene set label fontsize (default=8)</dd></dl>

Arguments

Plot enrichment results for hand picked gene sets — plot_select_sets

<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>factors_all</dt>
<dd>numeric Vector of one or more factor numbers to get plots for</dd>


<dt>sets_plot</dt>
<dd>character Vector of gene set names to show enrichment values for</dd>


<dt>color_sets</dt>
<dd>named character Values are colors corresponding to each set,
with names as the gene set names (default=NULL)</dd>


<dt>cl_rows</dt>
<dd>logical Set to TRUE to cluster gene set results (default=FALSE)</dd>


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


<dt>myfontsize</dt>
<dd>numeric Gene set label fontsize (default=8)</dd>

</dl>

plot_select_sets: Plot enrichment results for hand picked gene sets

Description

Usage

Value

Arguments