gssnng 0.2.6

Gene Set Scoring on the Nearest Neighbor Graph (gssnng)

gssnng

Try it out! ===>>>

See the paper ===>>> bioRxiv

Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq).

The problem: The sparsity of scRNA-seq data creates a poor overlap with many gene sets, which in turn makes gene set scoring difficult.

The GSSNNG method is based on using the nearest neighbor graph of cells for data smoothing. This essentially creates mini-pseudobulk expression profiles for each cell, which can be scored by using single sample gene set scoring methods often associated with bulk RNA-seq.

Nearest neighbor graphs (NNG) are constructed based on user defined groups (see the 'groupby' parameter below). The defined groups can be processed in parallel, speeding up the calculations. For example, a NNG could be constructed within each cluster or jointly by cluster and sample. Smoothing can be performed using either the adjacency matrix (all 1s) or the weighted graph to give less weight to more distant cells.

This package works with AnnData objects stored as h5ad files. Expression values are taken from adata.X. For creating groups, up to four categorical variables can be used, which are found in the adata.obs table.

Scoring functions work with ranked or unranked data ("your mileage may vary"):

Some method references (singscore, RBO) are below.

    singscore:            Normalised mean (median centered) ranks (requires ranked data)
    
    ssgsea:               The well known single sample GSEA.
        
    rank_biased_overlap:  RBO, Weighted average of agreement between sorted ranks and gene set.

    robust_std:     Med(x-med / mad), median of robust standardized values (recommend unranked).
    
    mean_z:         Mean( (x - mean)/stddv ), average z score. (recommend unranked).
    
    average_score:  Mean ranks or counts     
    
    median_score:   Median of counts or ranks
    
    summed_up:      Sum up the ranks or counts.

Installation from PyPI

pip3 install gssnng

Installation from GitHub

# also gets you the demo data and some gene sets.
git clone https://github.com/Gibbsdavidl/gssnng

pip install -e gssnng

Example script

Copy the script out from the cloned repo and run, check the paths if you get an error.

 cp gssnng/gssnng/test/example_script.py  .
 
 python3.8 test_gssnng.py

Usage

See gssnng/notebooks for examples on all methods

1. Read in an AnnData object using scanpy (an h5ad file).

2. Get your gene sets formatted as a .gmt file. (default is undirected, can take _UP, _DN, and split gene sets _UP+_DN)

3. Score cells, each gene set will show up as a column in adata.obs.

from gssnng import score_cells

q = sc.read_h5ad('gssnng/gssnng/test/data/pbmc3k_processed.h5ad')

sc.pp.neighbors(q, n_neighbors=32)

score_cells.with_gene_sets(adata=q,                            # AnnData object
                            gene_set_file='cibersort_lm22.gmt', # File path of gene sets
                            groupby='louvain',                  # Will sample neighbors within this group
                            smooth_mode='connectivity',         # Smooths matrix using distance weights from NN graph.
                            recompute_neighbors=0,              # Rebuild nearest neighbor graph with groups, 0 turns off function
                            score_method='singscore',           # Method of scoring
                            method_params={'normalization':'theoretical'},  # Special parameters for some methods 
                            samp_neighbors=27,                  # Number of sampled neighbors for pseudobulk
                            ranked=True,                        # Use ranked data, True or False
                            cores=8)                            # Groups are scored in parallel.
    

sc.pl.umap(q, color=['louvain','T.cells.CD8.up'], wspace=0.35)

Parameters

adata:  AnnData object from scanpy.read_*
AnnData containing the cells to be scored

gene_set_file: str[path]
The gene set file with list of gene sets, gmt, one per line. See `this definition <https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29>`_ .

groupby: [str, list, dict]
either a column label in adata.obs, and all categories taken, or a dict specifies one group.
SEE DESCRIPTION BELOW

smooth_mode: "adjacency" or "connectivity",
Dictates how to use the neighborhood graph.
`adjacency` weights all neighbors equally, `connectivity` weights close neighbors more

recompute_neighbors: int
should neighbors be recomputed within each group, 0 for no, >0 for yes and specifies N

score_method: str
which scoring method to use

method_params: dict
python dict with XGBoost params.

samp_neighbors: int
number of neighbors to sample

ranked: bool
whether the gene expression counts should be rank ordered

cores: int
number of parallel processes to work through groupby groups

Groupby

The specific neighborhood for each cell can be controlled by using the groupby parameter. In the example above, by setting groupby='louvain', only cells within a louvain cluster will be considered as being part of the neighborhood and will available for sampling. Groupby specifies a column name that's found in the AnnData.obs table, and it can also take a list of column names. In that case, cells will be grouped as the intersection of categories. For example, using groupby=['louvain','phenotype'] will take cells that are first in a given louvain cluster and then also in a given phenotype group. By also setting the recompute_neighbors, the nearest neighbor graph is recomputed within this subset of cells. Controlling the neighborhood leads to more controlled smoothing of the count matrix and is more suitable for downstream comparisons.

Gene sets

We are following the MSigDB nomenclature, where gene sets default to undirected, but can be marked with the suffix "_UP" (example: CD8_signature_UP or CD8.signature.up). In this case, when data is ranked, genes with higher expression have larger ranks. If the gene set has suffix "_DN" (example: CD8_signature_DN or CD8.signature.dn), then lowest expressed genes have largest ranks. In the use of singscore or Z scores, the undirected case is based on absolute values, so either direction, in the extreme, will result in a large score.

Method options

Some methods have some additional options. They are passed as a dictionary, method_params={param_name: param_value}.

singscore:  {'normalization': 'theoretical'}, {'normalization': 'standard'}

The singscore manuscript describes the theoretical method of standarization which involves determining the theoretical max and minimum ranks for the given gene set.

ssGSEA: {'omega': 0.25}

The ssGSEA method uses this parameter as a exponent to the ranks.

rank_biased_overlap:  {'rbo_depth': n}  (n: int)

Here, n is the depth that is decended down the ranks, where at each step, the overlap with the gene set is measured and added to the score.

The following methods do not have additional options.

robust_std
mean_z
average_score
median_score
summed_up

References

rank biased overlap: https://arxiv.org/pdf/1408.3587.pdf

singscore: https://pubmed.ncbi.nlm.nih.gov/30400809/

ssGSEA: https://gsea-msigdb.github.io/ssGSEA-gpmodule/v10/index.html

anndata: https://anndata.readthedocs.io/en/latest/

MSigDB: https://www.gsea-msigdb.org/gsea/msigdb/