Create barplot to visualize interaction changed features
plotICFSpot(
gobject,
icfObject,
source_type,
source_markers,
ICF_features,
cell_color_code = NULL,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "plotICFSpot"
)
giotto object
ICF (interaction changed feature) score object
cell type of the source cell
markers for the source cell type
named character vector of ICF features
cell color code for the interacting cell types
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
plot
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"
icfObject <- findInteractionChangedFeats(g,
cluster_column = "leiden_clus",
selected_feats = c("Gna12", "Ccnd2", "Btbd17"), nr_permutations = 10
)
#> Error in loadNamespace(x): there is no package called ‘future.apply’
plotICFSpot(
gobject = g, icfObject = icfObject,
source_type = "1", source_markers = "Ccnd2",
ICF_features = c("3" = "Gna12", "1" = "Ccnd2", "8" = "Btbd17")
)
#> Error in eval(expr, envir, enclos): object 'icfObject' not found