cluster cells using leiden methodology to visualize different resolutions
doGiottoClustree(
gobject,
res_vector = NULL,
res_seq = NULL,
return_gobject = FALSE,
show_plot = NULL,
save_plot = NULL,
return_plot = NULL,
save_param = list(),
default_save_name = "clustree",
verbose = TRUE,
...
)
giotto object
vector of different resolutions to test
list of float numbers indicating start, end, and step size for resolution testing, i.e. (0.1, 0.6, 0.1)
default FALSE. See details for more info.
by default, pulls from provided gobject instructions
by default, pulls from provided gobject instructions
by default, pulls from provided gobject instructions
list of saving parameters from
GiottoVisuals::all_plots_save_function()
name of saved plot, default "clustree"
be verbose
Arguments passed on to clustree::clustree
a plot object (default), OR a giotto object (if specified)
This function tests different resolutions for Leiden clustering and provides a visualization of cluster sizing as resolution varies.
By default, the tested leiden clusters are NOT saved to the Giotto object, and a plot is returned.
If return_gobject is set to TRUE, and a giotto object with all tested leiden cluster information will be returned.
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#>
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
doGiottoClustree(
gobject = g, res_vector = c(0.5, 0.8), return_plot = FALSE,
show_plot = FALSE, save_plot = FALSE
)
#> Error: package 'clustree' is not yet installed
#>
#> To install:
#> install.packages(c("clustree"))