simple_visNet: Simple graphs generation

In TianshuFeng/SemiMapper: Semi-supervised Topological Analysis

Simple graphs generation

Description

simple_visNet generates graphs from the provided Mapper object without tooltips.

Usage

simple_visNet(
  obj_mapper,
  filter = NULL,
  folder = getwd(),
  color_fun = color_map_Spectral,
  network_name = "network.html",
  color_filter = TRUE,
  groups_ind = NULL,
  color_code = NULL,
  color_mix = FALSE,
  save_network = TRUE,
  png_output = FALSE,
  layout_igraph = layout_with_fr
)

Arguments

obj_mapper	An object of class TDAmapper.
filter	A vector of filter values from filter functions
folder	The name of the folder to save the generated networks.
color_fun	The color function that transforms numbers to hex codes.
network_name	File name of the html network file.
color_filter	A logical object. TRUE if colors of nodes are to be determined by the average filter values of samples.
groups_ind	A vector of group names each of the samples belongs to.
color_code	A color code dataframe.
color_mix	Boolean. If to display the color of nodes as a mixer of the colors of samples within the nodes, where colors of samples are determined by their associated groups
save_network	Boolean. If save the network file. Used for the SHiny app

Details

simple_visNet generates graphs from the provided Mapper object without tooltips. The colors of nodes can be more flexibly defined than in network_visualization which is suitable for simulation and tests. The width of edges is propotional to the percentage of overlapping between connected nodes.

Users can assign colors to nodes with three different approaches.

• If color_filter=TRUE, the colors of nodes are determined by the average filter values of samples, and color_fun will map numeric values to hex color codes.

• If color_filter=FALSE and color_code=NULL, and groups_ind is provided, the colors of nodes are determined by the dominated group of samples according to groups_ind, and colors are automatically generated by color_fun.

• If color_filter=FALSE and color_code!=NULL, the colors of nodes are determined by the dominated group of samples, and colors are from color_code.

Note than the color method should be specified by the users by providing the function with necessary arguments.

Value

An HTML file saved under the location given in folder. The HTML file contains the interactive graph generated based on the Mapper object.

Examples

tp_data = chicken_generator(1)
tp_data_mapper = mapper.sta(dat = tp_data[,2:4],
                               filter_values = tp_data$Y,
                               num_intervals = 10,
                               percent_overlap = 70)
simple_visNet(tp_data_mapper, filter = tp_data$Y)

TianshuFeng/SemiMapper documentation built on Sept. 16, 2022, 10:26 p.m.