plotCPG: plotCPG

View source: R/spatial_interaction_visuals.R

plotCPGR Documentation

plotCPG

Description

Create visualization for cell proximity feature scores

Usage

plotCPG(...)

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.