propd Results TableBuilds a table of within-group and total log-ratio
variances, log-ratio means, and PALs (see: pals).
If the argument k is provided, the table will
label at most k top PALs. Just as each node
gets assigned a PAL, shale aims to assign
each edge a PAL. Edges that have a top PAL as one
and only one of their nodes get assigned that PAL.
Edges that have top PALs as both of their nodes
get assigned "Bridged". Edges without a top PAL
as one of their nodes will get assigned a PAL if
either (a) both nodes have the same neighbor PAL
or (b) one node has a "Missing" neighbor PAL.
The cutoff argument guides the maximum value of
theta above which to exclude the pair. A large integer
cutoff will instead retrieve the top N pairs as
ranked by theta.
shale(object, cutoff = 1000, k, prompt = TRUE, clean = FALSE)A propr or propd object.
For updateCutoffs, a numeric vector.
this argument provides the FDR cutoffs to test.
For graph functions, a numeric scalar. This argument
indicates the maximum theta to include in the figure.
For graph functions, a large integer will instead
retrieve the top N pairs as ranked by theta.
An integer. For propr methods, the number
of co-clusters (where all pairs receive a specified color
if and only if both members belong to same the cluster).
For propd methods, the maximum number of PALs to index
when calculating pals in the network.
A logical scalar. Set to FALSE to disable
the courtesy prompt when working with big data.
A boolean. Toggles whether to remove pairs
with "Bridged" or "Missing" PALs. Used by geyser,
bowtie, and gemini.