showPatternGenes

show genes correlated with spatial patterns

showPatternGenes(
  gobject,
  spatPatObj,
  dimension = 1,
  top_pos_genes = 5,
  top_neg_genes = 5,
  point_size = 1,
  return_DT = FALSE,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "showPatternGenes"
)

Arguments

gobject

giotto object

spatPatObj

Output from detectSpatialPatterns

dimension

dimension to plot genes for.

top_pos_genes

Top positively correlated genes.

top_neg_genes

Top negatively correlated genes.

point_size

size of points

return_DT

if TRUE, it will return the data.table used to generate the plots

show_plot

show plot

return_plot

return ggplot object

save_plot

directly save the plot [boolean]

save_param

list of saving parameters, see showSaveParameters

default_save_name

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

Value

ggplot