plotRankSpatvsExpr#

Last Updated: Mar 11, 2023

Description#

Plots dotplot to compare ligand-receptor rankings from spatial and expression information

Usage#

plotRankSpatvsExpr(
  gobject,
  combCC,
  expr_rnk_column = "LR_expr_rnk",
  spat_rnk_column = "LR_spat_rnk",
  midpoint = 10,
  size_range = c(0.01, 1.5),
  xlims = NULL,
  ylims = NULL,
  selected_ranks = c(1, 10, 20),
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotRankSpatvsExpr"
)

Arguments#

`gobject`	giotto object
`combCC`	combined communinication scores from `combCCcom`
`expr_rnk_column`	column with expression rank information to use
`spat_rnk_column`	column with spatial rank information to use
`midpoint`	midpoint of colors
`size_range`	size ranges of dotplot
`xlims`	x-limits, numerical vector of 2
`ylims`	y-limits, numerical vector of 2
`selected_ranks`	numerical vector, will be used to print out the percentage of top spatial ranks are recovered
`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#

ggplot