Pegasus for Single Cell Analysis
Pegasus is a tool for analyzing transcriptomes of millions of single cells. It is a command line tool, a python package and a base for Cloud-based analysis workflows.
Release Highlights in Current Stable
1.9.1 March 16, 2024
New Feature
Add
write_fgsea_results_to_excel
function (see documentation)
Improvement
For
dotplot
function, addshow_only_expressed
parameter to decide whether the color intensity of dots are based on cells expressing the genes to show or all cells. By default,show_only_expressed=True
. (PR 292)Allow
scatter
andspatial
functions to have a list ofvmin
andvmax
values when plotting multiple features.For
scatter
,spatial
,dotplot
,violin
functions, when some features are not in the data, emit a warning message and continue with features existing in the data.In
spatial
function, addnrows
andncols
to organize subplots.In
calculate_z_score
function, enforce the input count matrix to be dense orscipy.csr_matrix
.In
plot_gsea
function, addlabel_fontsize
parametere to allow change font label size in GSEA plots.
1.9.0 January 19, 2024
New Feature and Improvement
calculate_z_score
works with sparse count matrix. [PR 276 Thanks to Jayaram Kancherla]Plotting functions (
scatter
,dotplot
,violin
,heatmap
) now give warnings on genes/attributes not existing in the data, and skip them in the plots.Improve
heatmap
:Add
show_sample_name
parameter for cases of pseudo-bulk data, nanoString DSP data, etc.Use Scipy’s linkage (
scipy.cluster.hierarchy.linkage
) for dendrograms to use its optimal ordering feature for better results (seegroupby_optimal_ordering
parameter).
Update human lung and mouse immune markers used by
infer_cell_types
function.run_harmony
can accept multiple attributes to be the batch key, by providing a list of attribute names to itsbatch
parameter.Expose
online_batch_size
parameter innmf
andintegrative_nmf
functions.