viewHMRFresults_V2 — viewHMRFresults

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’)