Plots recovery plot to compare ligand-receptor rankings from spatial and expression information
giotto object
combined communication scores from combCCcom
column with expression rank information to use
column with spatial rank information to use
what to consider as ground truth (default: spatial)
logical. show plot
logical. return ggplot object
logical. save the plot
list of saving parameters, see
showSaveParameters
default save name for saving, don't change, change save_name in save_param
ggplot
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
#> python already initialized in this session
#> active environment : '/usr/bin/python3'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
exprCC <- exprCellCellcom(g,
cluster_column = "leiden_clus",
feat_set_1 = "Gm19935", feat_set_2 = "9630013A20Rik"
)
spatialCC <- spatCellCellcom(
gobject = g, cluster_column = "leiden_clus",
feat_set_1 = "Gm19935", feat_set_2 = "9630013A20Rik", verbose = "a lot",
random_iter = 10
)
#> Error: package 'future' is not yet installed
#>
#> To install:
#> install.packages(c("future"))
combCC <- combCCcom(spatialCC = spatialCC, exprCC = exprCC)
#> Error: object 'spatialCC' not found
plotRecovery(gobject = g, combCC = combCC)
#> Error: object 'combCC' not found