Create %>% graph objects for plotting different analysis subgroups.
create_networks.Rd
Create %>% graph objects for plotting different analysis subgroups.
Arguments
- e
experiment object
- correlation_list_name
(str) Name of the correlation list object used to generate the networks.
- channels
(str, default = c("cfos", "eyfp", "colabel")) The channels to process.
- alpha
(float, default = 0.05) The significance threshold for including brain regions in the network. if NULL or NA, this threshold is not applied.
- ontology
(str, default = "allen") Region ontology to use. options = "allen" or "unified"
- anatomical.order
(vec, c("Isocortex","OLF","HPF","CTXsp","CNU","TH","HY","MB","HB","CB")) The default super region acronym list that groups all subregions in the dataset.
- pearson_thresh
(float, default = 0.8) The pearson correlation coefficient threshold to apply for filtering out
- filter_isolates
(logical, default = FALSE) Whether to filter out the number of isolated (zero degree) nodes from the network. Default is to retain them.
Value
e experiment object. This object now has a new added element called networks.
This is a list storing a
graph object per channel for each network analysis run.
The name of each network (network_name
) is the same as the correlation_list_name
used to generate the network. This network_name
is fed as a parameter into the
plot_network()
function.