plot_gsea_hmap_w_similarity

Plot already computed enriched gene sets to show semantic similarity between 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_gsea_hmap_w_similarity 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 plot</dd>
<dt>direc</dt>
<dd>character Set to either 'up' or 'down' to use the appropriate sets</dd>
<dt>thresh</dt>
<dd>numeric Pvalue threshold to use for including gene sets in the heatmap</dd>
<dt>exclude_words</dt>
<dd>character Vector of words to exclude from word cloud
(default=character(0))</dd></dl>

Arguments

Plot already computed enriched gene sets to show semantic similarity between sets — plot_gsea_hmap_w_similarity

<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 plot</dd>


<dt>direc</dt>
<dd>character Set to either 'up' or 'down' to use the appropriate sets</dd>


<dt>thresh</dt>
<dd>numeric Pvalue threshold to use for including gene sets in the heatmap</dd>


<dt>exclude_words</dt>
<dd>character Vector of words to exclude from word cloud
(default=character(0))</dd>

</dl>

plot_gsea_hmap_w_similarity: Plot already computed enriched gene sets to show semantic similarity between sets

Description

Usage

Value

Arguments