| FELLA.USER-class {FELLA} | R Documentation |
An S4 class to save all the user analysis data
Assigning the value of show to a variable will provide
small data frames with the best scoring pathways (hypergeom)
and the best nodes in the KEGG network (diffusion and
pagerank)
"plot" is an S4 method to plot the results
from a FELLA.USER object
## S4 method for signature 'FELLA.USER'
show(object)
## S4 method for signature 'FELLA.USER,missing'
plot(x = new("FELLA.USER"),
method = "hypergeom", threshold = 0.05, plimit = 15, nlimit = 250,
layout = FALSE, thresholdConnectedComponent = 0.05,
LabelLengthAtPlot = 22, data = NULL, ...)
object |
A |
x |
A |
method |
Character, exactly one of:
|
threshold |
Numeric value between 0 and 1.
|
plimit |
Pathway limit, must be a numeric value between 1 and 50.
Limits the amount of pathways in |
nlimit |
Node limit, must be a numeric value between 1 and 1000.
Limits the order of the solution sub-graph when
in |
layout |
Logical, should the plot be returned as a layout? |
thresholdConnectedComponent |
Numeric value between 0 and 1. Connected components that are below the threshold are kept, while the ones exceeding it (because they are too small) are discarded. |
LabelLengthAtPlot |
Numeric value between 10 and 50. Maximum length that a label can reach when plotting the graph. The remaining characters will be truncated using "..." |
data |
FELLA.DATA object |
... |
Additional arguments passed to plotting functions |
show invisibly returns a list of data frames with the
best hits for each applied method
plot returns a layout if layout = T,
otherwise invisible()
userinputA U.userinput S4 object
hypergeomA U.hypergeom S4 object
diffusionA U.diffusion S4 object
pagerankA U.pagerank S4 object