Plot the networks stored in an experiment object
plot_joined_networks.Rd
Plot the networks stored in an experiment object
Usage
plot_joined_networks(
e,
correlation_list_names = c("male_agg", "female_non"),
title = NULL,
channels = "cfos",
absolute_weight = TRUE,
edge_colors = c(male_agg_pos = "#06537f", male_agg_neg = "#526c7a", female_non_pos =
"#C70039", female_non_neg = "#71585f"),
edge_color_labels = c(male_agg_pos = "Positive male", male_agg_neg = "Negative male",
female_non_pos = "Positive female", female_non_neg = "Negative female"),
height = 15,
width = 15,
region_legend = TRUE,
degree_scale_limit = c(1, 10),
correlation_edge_width_limit = c(0.8, 1),
image_ext = ".png",
network_radius = 300,
print_plot = TRUE,
graph_theme = NULL,
transparent_edge_group1 = TRUE,
transparent_edge_group2 = FALSE,
label_size = 5,
label_offset = 0.15,
save_plot = TRUE
)
Arguments
- e
experiment object
- correlation_list_names
(str vec) character vector of the two correlation lists used to include in a joined network, e.g.,
correlation_list_names = c("male_agg", "female_non")
- title
(str, default = NULL) Title of network plot
- channels
(str, default = c("cfos", "eyfp", "colabel"))
- absolute_weight
(bool, default = TRUE) Whether to plot absolute weights. If TRUE, the edge_colors and edge_colors_label should not contain values for positive and negative correlations.
- height
Height of the plot in inches.
- width
width of the plot in inches.
- region_legend
(default = TRUE) Boolean determining whether or not to show the region legend categorizing subregions into their largest parent region. Only works well if the Allen ontology is used for the dataset.
- degree_scale_limit
(vec, default = c(1,10)) Scale limit for degree size
- correlation_edge_width_limit
Can also be a hexadecimal color code written as a string.
- image_ext
(default = ".png") image extension to the plot as.
- print_plot
(bool, default = TRUE) Whether to print the plot as an output. the experiment object output folder.
- graph_theme
(default = NULL) Add a
ggraph::theme()
to the network graph. If NULL, the default is taken.- label_size
(default = 5) Default font size for network region labels.
- label_offset
(default = 0.15) Distance of label from nodes.
- save_plot
(bool, default = TRUE) Save into the figures subdirectory of the the experiment object output folder.
- edge_color
(str, default = c(male_agg_pos = "Positive male", male_agg_neg = "Negative male", female_non_pos = "Positive female", female_non_neg = "Negative female")) Color of the network edges as a named vector.