Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST
The simulated dataset examples were in ./Simulation/simulated_datasets folder.
Brief descriptions of simulated scripts (./Simulation/Rcode folder):
simulated_Scenario1_low(middle,high).R: Integration data analysis for Scenario 1 with three different batch effects' scales.
simulated_Scenario2_low(middle,high).R: Integration data analysis for Scenario 2 with three different batch effects' scales.
simulated_Scenario3.R: Integrative data analysis for Scenario 3.
simulated_Scenario4.R: Integrative data analysis for Scenario 4.
simulated_Scenario5.R: Integrative data analysis for Scenario 5.
Brief descriptions of real data analysis scripts (Real_data_analysis folder):
HCC and mouse liver data: Four HCC sections are available in the data folder. The count matrix is stored in the SeuratObject HCCx_seu.RDS, while the metadata and manual annotations (manual.annotation) are saved in meta.data_HCCx.csv. Additionally, eight mouse liver sections are stored in the SeuratObject seulist_mouseLiverST8.RDS, which can be directly loaded into R using the readRDS() function.
dorsolateral_prefrontal_cortex.R: Integration data analysis for human dorsolateral prefrontal cortex Visium data
mouse_liver.R: Integration data analysis for mouse liver ST data
olfactory_bulb.R: Integration data analysis for mouse olfactory bulb Slide-seqV2 data
hepatocellular_carcinoma.R: Integration data analysis for hepatocellular carcinoma Visium data
The real data results were visualized with ggplot2 package (Real_data_results folder).
Brief descriptions of real data viualization scripts:
dorsolateral_prefrontal_cortex_viualize.R: Visualization for human dorsolateral prefrontal cortex Visium data
mouse_liver_viualize.R: Visualization for mouse liver ST data
olfactory_bulb_viualize.R: Visualization for mouse olfactory bulb Slide-seqV2 data
hepatocellular_carcinoma_viualize.R: Visualization for hepatocellular carcinoma Visium data