Create a joined network to visualize overlapping connections with the same outer joined node set.
create_joined_networks.Rd
Create a joined network to visualize overlapping connections with the same outer joined node set.
Usage
create_joined_networks(
e,
correlation_list_names = c("male_agg", "female_non"),
channels = "cfos",
ontology = "unified",
alpha = 0.001,
pearson_thresh = 0.9,
alpha2 = NULL,
pearson_thresh2 = NULL,
anatomical.order = c("Isocortex", "OLF", "HPF", "CTXsp", "CNU", "TH", "HY", "MB",
"HB", "CB"),
export_overlapping_edges = TRUE
)
Arguments
- e
experiment object
- correlation_list_names
(str vec) character vector of the two correlation lists used to include in a joined network
- channels
(str, default = c("cfos", "eyfp", "colabel")) The channels to process.
- ontology
(str, default = "allen") Region ontology to use. options = "allen" or "unified"
- alpha
(float, default = 0.05) The significance threshold for including brain regions in the network. if NULL or NA, this threshold is not applied.
- pearson_thresh
(float, default = 0.8) The pearson correlation coefficient threshold to apply for filtering out
- alpha2
(NULL) If not NULL, this gives the option of filtering the second network by a different alpha from the first. The
alpha
parameter will then be used as the threshold for network 1.- pearson_thresh2
(NULL) If not NULL, this gives the option of filtering the second network by a different pearson threshold from the first network. The
pearson_thresh
parameter will then be used as the threshold for network 1.- 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.
- export_overlapping_edges
(bool, default = TRUE) Whether to export the overlapping edges between the two networks as a csv into the
table
directory.
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.