Create visualization for cell proximity feature scores
plotCPF(
gobject,
icfObject,
method = c("volcano", "cell_barplot", "cell-cell", "cell_sankey", "heatmap", "dotplot"),
min_cells = 5,
min_cells_expr = 1,
min_int_cells = 3,
min_int_cells_expr = 1,
min_fdr = 0.05,
min_spat_diff = 0.2,
min_log2_fc = 0.2,
min_zscore = 2,
zscores_column = c("cell_type", "feats"),
direction = c("both", "up", "down"),
cell_color_code = NULL,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "plotCPG"
)giotto object
ICF (interaction changed feature) score object
plotting method to use
minimum number of source cell type
minimum expression level for source cell type
minimum number of interacting neighbor cell type
minimum expression level for interacting neighbor cell type
minimum adjusted p-value
minimum absolute spatial expression difference
minimum log2 fold-change
minimum z-score change
calculate z-scores over cell types or features
differential expression directions to keep
character. discrete colors to use. palette to use or named vector of colors
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",
selected_feats = c("Gna12", "Ccnd2", "Btbd17"), nr_permutations = 10
)
#> Error in loadNamespace(x): there is no package called ‘future.apply’
plotCPF(
gobject = g, icfObject = icfObject, show_plot = TRUE,
save_plot = FALSE, return_plot = FALSE
)
#> Error: object 'icfObject' not found