Create a tree from an STGrid object

Create a tree from an STGrid object

# S4 method for STGrid
hc_tree(
  object,
  method = c("complete", "ward.D", "ward.D2", "single", "average", "mcquitty", "median",
    "centroid"),
  layout = c("circular", "rectangular", "slanted", "fan", "unrooted", "time-scale",
    "two-dimensional"),
  dist_method = "pearson",
  branch_length = "none",
  class_nb = 1,
  class_name = NULL,
  size = 2.25,
  colors = NULL,
  class_label = TRUE,
  offset = 5,
  offset.text = 1.5,
  lab_fontsize = 3.88,
  lab_barsize = 2,
  geom_label = c("text", "label", "shadowtext"),
  no_legend = FALSE,
  return_tree = FALSE
)

Arguments

object

The STGrid object

method

The agglomeration method to be used. See stats::hclust().

layout

The layout to be used See ggtree::ggtree().

dist_method

The method for distance computation. See stats::cor().

branch_length

A variable for scaling branch, if 'none' draw cladogram. See ggtree::ggtree().

class_nb

An integer indicating the desired number of groups.

class_name

A set of names for the classes.

size

The size of the labels.

colors

A set of colors for the classes.

class_label

Whether to add class labels.

offset

Offset of labels from the clade

offset.text

Offset of text labels from the bar.

lab_fontsize

Label font size.

lab_barsize

Bar label size.

geom_label

Label fomat.

no_legend

Whether to discard legend.

return_tree

Logical. Whether to return the tree not the plot. In fact a list with the tree and associated clusters.

Examples

example_dataset()
#> |-- INFO :  Dataset 11284233/files/Xenium_Mouse_Brain_Coronal_7g was already loaded. 
p <- hc_tree(Xenium_Mouse_Brain_Coronal_7g, class_nb = 4, class_name = letters[1:4])
#> |-- INFO :  Using complete method 
#> |-- INFO :  Using circular layout 
print(p)

# Get classes:
p$tree_classes
#> $MOD1
#> [1] "Ano1"
#> 
#> $MOD2
#> [1] "Chat"
#> 
#> $MOD3
#> [1] "Ebf3"
#> 
#> $MOD4
#> [1] "Kctd8"  "Necab2" "Nrp2"   "Nwd2"  
#>