plotCellProximityFeatSpot: plotCellProximityFeatSpot

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

plotCellProximityFeatSpot

Description

Create visualization for cell proximity feature scores

Usage

plotCellProximityFeatSpot(
  gobject,
  icfObject,
  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", "features"),
  direction = c("both", "up", "down"),
  cell_color_code = NULL,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotCellProximityFeats"
)

Arguments

gobject	giotto object
icfObject	ICF (interaction changed feature) score object
method	plotting method to use
min_cells	minimum number of source cell type
min_cells_expr_resi	Default = 0.05
min_int_cells	minimum number of interacting neighbor cell type
min_int_cells_expr_resi	Default = 0.05
min_fdr	minimum adjusted p-value
min_pcc_diff	Default = 0.05
min_zscore	minimum z-score change
zscores_column	calculate z-scores over cell types or features
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

plot

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.