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SpaTalk functions

SpaTalk package consists of five types of functions, namely the Datasets, Preprocessing, Main, Visulization, Demo-data.

Please refer to the tutorial vignette with demo data processing steps. Detailed functions see the document

Datasets

• geneinfo Gene symbols of Human and Mouse updated on June 30, 2021 for revising count matrix

  • Use customed geneinfo

• lrpairs Ligand-receptor pairs of Humanand Mouse containing 3398 human and 2033 mouse pairs

  • Use customed lrpairs

• pathways KEGG pathways and Reactomes of Human and Mouse for intra-cellular genes and transcription factors

  • Use customed pathways

Preprocessing

• rev_gene() Revise gene symbols

• generate_spot() Generate pseudo spot st_data with single-cell st_data

• createSpaTalk() Create SpaTalk object using spatial transcriptomics data

Main

• dec_celltype() Identify the cellular composition with non-negative regression

• find_lr_path() Find downstream targets and transcriptional factors for receptors

• dec_cci() Identify the cell-cell communications

• dec_cci_all() Identify the all cell-cell communications

• get_lr_path() Get LR and downstream pathways

• set_expected_cell() Set the expected cell for each spot.

Visulization

• plot_st_pie_generate() Plot scatterpie for data generated from generate_spot()

• plot_st_pie() Plot scatterpie for spot-based ST data SpaTalk object

• plot_st_gene() Point plot with spatial distribution of a gene

• plot_st_gene() Point plot with spatial distribution of a gene

• plot_st_celltype() Ponit plot with spatial distribution of a single predicted cell type

• plot_st_celltype_density() Plot spatial density of a single predicted cell type

• plot_st_celltype_density() Plot spatial density of a single predicted cell type

• plot_st_celltype_percent() Ponit plot with spatial distribution of a single predicted cell type percent

• plot_st_celltype_all() Ponit plot with spatial distribution of all predicted cell types

• plot_st_cor_heatmap() Heatpmap of correlation between marker gene expression and cell type percent

Visulization (cell-cell communications)

• plot_ccdist() Point plot with spatial distribution of celltype_sender and celltype_receiver

• plot_cci_lrpairs(type = "sig") Heatmap with LR pairs of celltype_sender and celltype_receiver

• plot_cci_lrpairs(type = "number") Heatmap with the number of spatial LRI pairs of celltype_sender and celltype_receiver

• plot_lrpair() Point plot with LR pair from celltype_sender to celltype_receiver

• plot_lrpair_vln() Violin plot spatial distance of LR pair between senders and receivers and between all cell-cell pairs

• plot_lr_path() Plot network with LR and downstream pathways

• plot_path2gene() River plot of significantly activated pathways and related downstream genes of receptors

Demo-data

• demo_st_data() demo spot-based ST data

• demo_st_meta() demo spot-based ST meta

• demo_st_sc_data() demo single-cell ST data

• demo_st_sc_meta() demo single-cell ST meta

• demo_sc_data() demo scRNA-seq data

• demo_geneinfo() demo geneinfo

• demo_lrpairs() demo lrpairs

• demo_pathways() demo pathways

• demo_dec_result() demo dec_result