Launch ShinyCAT: Cnet Adjustment Tool

Launch ShinyCAT: Cnet Adjustment Tool

Usage

launch_shinycat(g = NULL, envir = new.env(), ..., options = list(width = 1200))

Arguments

g

igraph object, or can be NULL if the variable 'g' is defined in 'envir'.

envir

environment assigned to the R-shiny function space, which may be useful when capturing the igraph object after manipulation via the R-shiny app.

...

additional arguments are ignored.

options

list with additional settings, for example:

• host: character string with hostname or IP address to permit incoming connections. Use '0.0.0.0' to accept all incoming host names.

• port: numerical port to listen for incoming connections.

• quiet: logical whether to

• launch.browser: logical whether to launch a web browser, default TRUE for interactive sessions.

• display.mode: character string with display mode: 'normal' is recommended; 'showcase' displays the code beside the app.

Value

environment invisibly, containing

• 'g' the input igraph

• 'adj_cnet' the output igraph after manipulation in the R-shiny app. It also contains two attributes for reference:

  1. 'nodeset_adj': data.frame used to adjust nodesets.

  2. 'node_adj': data.frame used to adjust nodes.

Details

This function launches the R-shiny app 'ShinyCat' to manipulate a Cnet igraph object, which is expected to contain node (vertex) attribute 'nodeType' with values 'Gene' and 'Set'.

There are two ways to retain the resulting igraph object:

1. Capture the output of this function, an environment described below.

2. Click "Adjustments" then "Save RData", which stores the 'igraph` object as 'adj_cnet'.

The function returns an environment inside which are two objects:

• 'g': the igraph data input

• 'adj_cnet': the adjusted Cnet igraph output

Additionally, the 'adj_cnet' object contains two attributes:

• 'nodeset_adj', 'node_adj': data.frame objects used by bulk_cnet_adjustments() to convert 'g' into 'adj_cnet'.

See also

Other jam igraph utilities: color_edges_by_nodegroups(), color_edges_by_nodes(), color_nodes_by_nodegroups(), get_cnet_nodeset(), jam_igraph(), subgraph_jam()

Other jam cnet utilities: adjust_cnet_nodeset(), adjust_cnet_set_relayout_gene(), apply_nodeset_spacing(), bulk_cnet_adjustments(), get_cnet_nodeset(), make_cnet_test()

Other jam shiny functions: shinycat_server(), shinycat_ui()

Examples

# create Cnet test data
g <- make_cnet_test();
cnetenv <- new.env();

# you must catch the output to use the resulting igraph object
# output_envir <- launch_shinycat();