This package provides plotting scripts for the figures presented in the Optocoder paper. Data presented in the paper are generated with Optocoder v0.1.1. The data can be downloaded from: https://doi.org/10.5281/zenodo.6492306

Samples to run described in: samples_inhouse_figures_revision.yaml and samples_slideseq_figures_revision.yaml files. PLease make sure that download files' paths are correctly set in the test_run yaml files. Then basically run:

python3 plot_paper_figures.py -sample_list samples_inhouse_figures_revision.yaml

Figures metadata can be found below.

	Description	Used Pucks	FLAG
Fig. 1	Optocoder pipeline.	Sketch. Microscopy images are from P4.	NA
Fig. 2	Crosstalk correction	a) Sketch. b) Data from P4.	PLOT_CROSSTALK
Fig. 3	Phasing/prephasing	Sketch. No data is used.	NA
Fig. 4	Machine learning pipeline	Sketch. No data is used.	NA
Fig. 5	Matching results.	P1, P2, P3, P4.	PLOT_MATCHES
Fig. 6	Matching results (Slide-Seq)	SSP1, SSP2, SSP3, SSP4.	PLOT_MATCHES
Sup. Fig. 1	QC Plots	P4	Optocoder
Sup. Fig. 2	QC Plots	P4	Optocoder
Sup. Fig. 3	Image processing	P4	Optocoder
Sup. Fig. 4	Phasing heatmap	P1, P2, P3, P4	PLOT_PHASING_SEARCH
Sup. Fig. 5	Phasing heatmap	SSP1, SSP2, SSP3, SSP4	PLOT_PHASING_SEARCH
Sup. Fig. 6	ML Comparisons	a) P1, P2, P3, P4 b) SSP1, SSP2, SSP3, SSP4	PLOT_ML_COMPARISON
Sup. Fig. 7	ML Specificity Analysis	a) P1, P2, P3, P4 b) SSP1, SSP2, SSP3, SSP4	PLOT_ML_SPECIFICITY_ANALYSIS
Sup. Fig. 8	Top Barcodes Analysis	a) P1, P2, P3, P4 b) SSP1, SSP2, SSP3, SSP4	PLOT_TOP_BARCODES_ANALYSIS
Sup. Fig. 9	Chastity Score Analysis	a) P1, P2, P3, P4 b) SSP1, SSP2, SSP3, SSP4	PLOT_CHASTITY_ANALYSIS
Sup. Fig. 10	Prediction Score Analysis	a) P1, P2, P3, P4 b) SSP1, SSP2, SSP3, SSP4	PLOT_CHASTITY_ANALYSIS