viewHMRFresults_V2

Source: R/python_hmrf.R

function to view HMRF results with multiple betas

viewHMRFresults_V2(
  gobject,
  k,
  betas,
  hmrf_name,
  spat_unit = NULL,
  feat_type = NULL,
  third_dim = FALSE,
  cow_n_col = 2,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = TRUE,
  save_plot = TRUE,
  return_plot = TRUE,
  default_save_name = "HMRF_result",
  save_param = list(),
  ...
)

Arguments

gobject

giotto object

k

number of clusters in hmrf results

betas

values of beta to plot

hmrf_name

name of hmrf models

spat_unit

spatial unit

feat_type

feature type

third_dim

index of 3D plot

cow_n_col

number of columns to show in figure

cow_rel_h

relative height

cow_rel_w

relative width

cow_align

cowplot alignment parameter

show_plot

option to show plot

save_plot

option to save plot

return_plot

if function return a plot

default_save_name

names of figure file to save

save_param

other saving parameters

...

additional params to pass to plotting

Value

spatial plots with HMRF domains

Details

This function plots spatial map of HMRF domain clusters for multiple beta with the name (hmrf_name), matching the first part of the cell meta column names with HMRF clusters (for example name of ‘hmrf1 k=8 b=0.00’ is ‘hmrf1’)