plotCellProximityGenesSpot: plotCellProximityGenesSpot

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

plotCellProximityGenesSpot

Description

Create visualization for cell proximity gene scores

Usage

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"
)

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_int_cells	minimum number of interacting neighbor cell type
min_fdr	minimum adjusted p-value
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
min_cells_expr	minimum expression level for source cell type
min_int_cells_expr	minimum expression level for interacting neighbor cell type
min_spat_diff	minimum absolute spatial expression difference
min_log2_fc	minimum log2 fold-change

Value

plot

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.