summarize.microNetComp: Summary Method for Objects of Class microNetComp

In stefpeschel/NetCoMi: Network Construction and Comparison for Microbiome Data

Summary Method for Objects of Class microNetComp

Description

The main results returned by netCompare are printed in a well-arranged format.

Usage

## S3 method for class 'microNetComp'
summary(
  object,
  groupNames = NULL,
  showCentr = "all",
  numbNodes = 10L,
  showGlobal = TRUE,
  showGlobalLCC = TRUE,
  showJacc = TRUE,
  showRand = TRUE,
  showGCD = TRUE,
  pAdjust = TRUE,
  digits = 3L,
  digitsPval = 6L,
  ...
)

## S3 method for class 'summary.microNetComp'
print(x, ...)

Arguments

object	object of class microNetComp returned by netCompare.
groupNames	character vector with two elements giving the group names for the two networks. If NULL, the names are adopted from object.
showCentr	character vector indicating which centrality measures should be included in the summary. Possible values are "all", "degree", "betweenness", "closeness", "eigenvector" and "none".
numbNodes	integer indicating for how many nodes the centrality values shall be printed. Defaults to 10 meaning that the first 10 taxa with highest absolute group difference of the specific centrality measure are shown.
showGlobal	logical. If TRUE, global network properties for the whole network are printed.
showGlobalLCC	logical. If TRUE, global network properties for the largest connected component are printed. If the network is connected (number of components is 1) the global properties are printed only once (if one of the arguments showGlobal and showGlobalLCC) is TRUE.
showJacc	logical. If TRUE, the Jaccard index is printed.
showRand	logical. If TRUE, the adjusted Rand index (if existent) is returned.
showGCD	logical. If TRUE, the Graphlet Correlation Distance (if existent) is printed.
pAdjust	logical. The permutation p-values (if existent) are adjusted if TRUE (default) and not adjusted if FALSE.
digits	integer giving the number of decimal places to which the results are rounded. Defaults to 3L.
digitsPval	integer giving the number of decimal places to which the p-values are rounded. Defaults to 6L.
...	not used.
x	object of class summary.microNetComp (returned by summary.microNetComp).

See Also

netCompare

stefpeschel/NetCoMi documentation built on Feb. 4, 2024, 8:20 a.m.