plotRankSpatvsExpr: plotRankSpatvsExpr

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

plotRankSpatvsExpr

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

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