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" )
| 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 |
| default_save_name | default save name for saving, don't change, change save_name in save_param |
plot