Create visualization for cell proximity gene scores
plotCellProximityGenesSpot(
gobject,
cpgObject,
method = c("volcano", "cell_barplot", "cell-cell", "cell_sankey", "heatmap",
"dotplot"),
min_cells = 4,
min_cells_expr_resi = 0.05,
min_int_cells = 4,
min_int_cells_expr_resi = 0.05,
min_fdr = 0.5,
min_pcc_diff = 0.05,
min_zscore = 0.05,
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 number of interacting neighbor cell type
minimum adjusted p-value
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
minimum expression level for source cell type
minimum expression level for interacting neighbor cell type
minimum absolute spatial expression difference
minimum log2 fold-change
plot