tandem MS data

plot_correlation_network

R Documentation

Plot an interactive correlation network with communities highlighted

Description

Plot an interactive correlation network with communities highlighted

Usage

plot_correlation_network(
  res,
  idx = NULL,
  source = "name_1",
  target = "name_2",
  cluster = NULL,
  df_corr = NULL,
  var_p_val = "p_corr",
  var_r_corr = "r_corr",
  r_corr_thresh = 0.8,
  p_val_thresh = 0.05,
  ...
)

Arguments

`res`	an `InteRactome`
`idx`	indexes of the set of proteins in `res` for which correlations will be computed.
`source`	variable of `df_corr` with the names of the source protein
`target`	variable of `df_corr` with the names of the target protein
`cluster`	named vector containing the cluster number for each node
`df_corr`	a data.frame with columns 'r_corr' and 'p_corr'. Has priority over parameters `res`.
`var_p_val`	variable for which the threshold `p_val_thresh` will be applied. Set to 'p_corr' by default
`var_r_corr`	variable for which the threshold `r_corr_thresh` will be applied. Set to 'r_corr' by default
`r_corr_thresh`	threshold for variable 'r_corr' (min)
`p_val_thresh`	threshold for variable `var_p_val` (max)
`...`	other parameters passed either to function `compute_correlations()` if `df_corr` is NULL or to function `restrict_network_degree()` otherwise.