Home

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 (cell types)

• 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() Heatmap with LR 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