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()
userinput
A U.userinput
S4 object
hypergeom
A U.hypergeom
S4 object
diffusion
A U.diffusion
S4 object
pagerank
A U.pagerank
S4 object