Create visualization for cell proximity feature scores
plotCellProximityFeatSpot(
gobject,
icfObject,
method = c("volcano", "cell_barplot", "cell-cell", "cell_sankey", "heatmap", "dotplot"),
min_cells = 4,
min_cells_expr_resi = 0.05,
min_int_cells = 4,
min_int_cells_expr_resi = 0.05,
min_fdr = 0.5,
min_pcc_diff = 0.05,
min_zscore = 0.05,
zscores_column = c("cell_type", "features"),
direction = c("both", "up", "down"),
cell_color_code = NULL,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "plotCellProximityFeats"
)giotto object
ICF (interaction changed feature) score object
plotting method to use
minimum number of source cell type
Default = 0.05
minimum number of interacting neighbor cell type
Default = 0.05
minimum adjusted p-value
Default = 0.05
minimum z-score change
calculate z-scores over cell types or features
differential expression directions to keep
vector of colors with cell types as names
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
#> 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"
icfObject <- findInteractionChangedFeats(g, cluster_column = "leiden_clus")
#> Error in loadNamespace(x): there is no package called ‘future.apply’
plotCellProximityFeatSpot(
gobject = g, icfObject = icfObject,
show_plot = TRUE, save_plot = FALSE, return_plot = FALSE,
min_pcc_diff = 0.01
)
#> Error: object 'icfObject' not found