plot_gene_haystack

plot_gene_haystack.matrix

plot_gene_haystack.data.frame

plot_gene_haystack.SingleCellExperiment

plot_gene_haystack.Seurat

Visualizing the detection/expression of a gene in a 2D plot

One key exploratory analysis step in single-cell genomics data analysis
is the prediction of features with different activity levels. For example, we want
to predict differentially expressed genes (DEGs) in single-cell RNA-seq data,
spatial DEGs in spatial transcriptomics data, or differentially accessible
regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially
active features in single cell omics datasets without relying on the clustering
of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler
divergence to find features (e.g., genes, genomic regions, etc) that are active
in subsets of cells that are non-randomly positioned inside an input space (such as
1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For
the theoretical background of 'singleCellHaystack' we refer to our original paper
Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3>
and our update Vandenbon and Diez (Scientific Reports, 2023) <doi:10.1038/s41598-023-38965-2>.

Alexis Vandenbon

singleCellHaystack

A Universal Differential Expression Prediction Tool for
Single-Cell and Spatial Genomics Data

Diego Diez

plot_gene_haystack function

<dl><dt>x</dt>
<dd>a matrix or other object from which coordinates of cells can be extracted.</dd>
<dt>...</dt>
<dd>further parameters passed to plot_gene_haystack_raw().</dd>
<dt>dim1</dt>
<dd>column index or name of matrix for x-axis coordinates.</dd>
<dt>dim2</dt>
<dd>column index or name of matrix for y-axis coordinates.</dd>
<dt>assay</dt>
<dd>name of assay data for Seurat method.</dd>
<dt>coord</dt>
<dd>name of coordinates slot for specific methods.</dd>
<dt>slot</dt>
<dd>name of slot for assay data for Seurat method.</dd></dl>

Arguments

Visualizing the detection/expression of a gene in a 2D plot — plot_gene_haystack

<dl>

<dt>x</dt>
<dd>a matrix or other object from which coordinates of cells can be extracted.</dd>


<dt>...</dt>
<dd>further parameters passed to plot_gene_haystack_raw().</dd>


<dt>dim1</dt>
<dd>column index or name of matrix for x-axis coordinates.</dd>


<dt>dim2</dt>
<dd>column index or name of matrix for y-axis coordinates.</dd>


<dt>assay</dt>
<dd>name of assay data for Seurat method.</dd>


<dt>coord</dt>
<dd>name of coordinates slot for specific methods.</dd>


<dt>slot</dt>
<dd>name of slot for assay data for Seurat method.</dd>

</dl>

plot_gene_haystack: Visualizing the detection/expression of a gene in a 2D plot

Description

Usage

Arguments