Visualize Cell Proximity Gene Scores

plotCellProximityGenes()

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"
)

Arguments

gobject	giotto object
cpgObject	ICG (interaction changed gene) 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 genes
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

Value

A plot.