Create visualization for cell proximity gene scores
plotCellProximityGenes(
gobject,
cpgObject,
method = c("volcano", "cell_barplot", "cell-cell", "cell_sankey", "heatmap",
"dotplot"),
min_cells = 4,
min_cells_expr = 1,
min_int_cells = 4,
min_int_cells_expr = 1,
min_fdr = 0.1,
min_spat_diff = 0.2,
min_log2_fc = 0.2,
min_zscore = 2,
zscores_column = c("cell_type", "genes"),
direction = c("both", "up", "down"),
cell_color_code = NULL,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "plotCellProximityGenes"
)giotto object
ICG (interaction changed gene) score object
plotting method to use
minimum number of source cell type
minimum expression level for source cell type
minimum number of interacting neighbor cell type
minimum expression level for interacting neighbor cell type
minimum adjusted p-value
minimum absolute spatial expression difference
minimum log2 fold-change
minimum z-score change
calculate z-scores over cell types or genes
differential expression directions to keep
vector of colors with cell types as names
show plots
return plotting object
directly save the plot [boolean]
list of saving parameters from all_plots_save_function
default save name for saving, don't change, change save_name in save_param
plot