Mosaic API documentation

Older documentations

The latest version of Mosaic is recommended for new developments. Documentation for the other versions are available for applications and notebooks built using them: v3.7.0r1 (first documentation revision of v3.7.0) , v3.4.0 , v3.1.1 , v2.4.1 , v1.8.0

Mosaic is a set of tools to analyze DNA and protein data obtained from the Mission Bio Tapestri instrument. Its designed to allow convenient handling and visualization of single-cell multiomics data to enable exploratory analysis.

Basic Classes

_Assay	Abstract class for all assays
Dna	Container for DNA data.
Cnv	Container for CNV data.
Protein	Container for Protein data
Sample	Container for multiple assays.
SampleGroup	A group of samples related to each other

Interactive Workflows

CopyNumber	Copy Number estimation workflow.
VariantSubcloneTable	To provide as much similarity to Tapestri Insights as possible.

Algorithms

NSP([jitter, random_state, sample_size, ...])	Noise corrected and Scaled Protein counts (NSP)
GroupByGenotype(dna, features[, layer, ...])	See group_by_genotype() for the complete documentation
COMPASS(sample, somatic_variants[, ...])	A wrapper to run COMPASS.

Functional Modules

io	Module to read and write h5 files
utils	Utility functions
constants	Keys used for various layers, row attributes and column attributes

Custom Plots

Heatmap	Heatmap with options for grouping rows/cols.
LinePlot	A line plot to visualize CNV.
BarGraph	Create a horizontal bar graph with ticks and labels.
MultiMap	Multiple heatmaps with a common y-axis.
PhyloTree	Container for creating a phylogenetic tree.
Fishplot	Container for creating a fishplot.

DNA Assignment

Truth	Truth data for GT demultiplexing
LikelihoodMethod	A likelihood-based demultiplexing method for DNA data.
DnaAssignment	A wrapper for the missionbio.demultiplex module.

Protein Assignment

Truth	A phylogenetic tree of cell types.
LikelihoodMethod	A PACE method to categorize the cells into the most likely category based on the given truth.
ProbabilityMethod	A PACE method to categorize the cells into the mot probable category based on the given truth.