plotCellProximityFeats#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L1166

Description#

Create visualization for cell proximity feature scores

Usage#

plotCellProximityFeats(
  gobject,
  icfObject,
  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", "feats"),
  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#

Argument

Description

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

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 featuress

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_f unction <#allplotssavefunction>`__

default_save_name

default save name for saving, don’t change, change save_name in save_param

Value#

plot