plotRankSpatvsExpr#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L2383

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#

Argument

Description

gobject

giotto object

combCC

combined communinication scores from `combCCcom <#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_f unction <#allplotssavefunction>`__

default_save_name

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

Value#

ggplot