plotCellProximityGenes: plotCellProximityGenes

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

plotCellProximityGenes

Description

Create visualization for cell proximity feature scores

Usage

plotCellProximityGenes(...)

Arguments

...

Arguments passed on to plotCellProximityFeats gobject giotto object icfObject ICF (interaction changed feature) score object method plotting method to use min_cells minimum number of source cell type min_cells_expr minimum expression level for source cell type min_int_cells minimum number of interacting neighbor cell type min_int_cells_expr minimum expression level for interacting neighbor cell type min_fdr minimum adjusted p-value min_spat_diff minimum absolute spatial expression difference min_log2_fc minimum log2 fold-change min_zscore minimum z-score change zscores_column calculate z-scores over cell types or featuress direction differential expression directions to keep cell_color_code vector of colors with cell types as names show_plot show plots return_plot return plotting object save_plot directly save the plot [boolean] save_param list of saving parameters from all_plots_save_function default_save_name default save name for saving, don't change, change save_name in save_param

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.