Description Usage Arguments Details Author(s) See Also Examples
Functions to plot the subgraphs induced by the most significant GO terms
1 2 3 4 5 6 7 8 | showSigOfNodes(GOdata, termsP.value, firstSigNodes = 10, reverse = TRUE,
sigForAll = TRUE, wantedNodes = NULL, putWN = TRUE,
putCL = 0, type = NULL, showEdges = TRUE, swPlot = TRUE,
useFullNames = TRUE, oldSigNodes = NULL,
useInfo = c("none", "pval", "counts", "def", "np", "all")[1],
plotFunction = GOplot, .NO.CHAR = 20)
printGraph(object, result, firstSigNodes, refResult, ...)
|
object |
an object of class |
GOdata |
an object of class |
result |
an object of class |
firstSigNodes |
the number of top scoring GO terms which .... |
refResult |
an object of class |
termsP.value |
named vector of p-values. |
reverse |
the direction of the edges. |
sigForAll |
if |
wantedNodes |
the nodes that we want to find, we will plot this nodes with a different color. The vector contains the names of the nodes |
putWN |
the graph is generated with using the firstSigNodes and the wantedNodes. |
putCL |
we generate the graph from the nodes given by all previous parameters, plus their children. if putCL = 1 than only the children are added, if putCL = n we get the nodes form the next n levels. |
type |
used for ploting pie charts |
showEdges |
if |
swPlot |
if true the graph is ploted, if not no ploting is done. |
useInfo |
aditional info to be ploted to each node. |
oldSigNodes |
used to plot the (new) sigNodes in the same collor range as the old ones |
useFullNames |
argument for internal use .. |
plotFunction |
argument for internal use .. |
.NO.CHAR |
argument for internal use .. |
... |
Extra arguments for
|
There are two functions available. The showSigOfNodes
will plot
the induced subgraph to the current graphic device. The
printGraph
is a warping function for showSigOfNodes
and
will save the resulting graph into a PDF or PS file.
In the plots, the significant nodes are represented as rectangles. The plotted graph is the upper induced graph generated by these significant nodes.
Adrian Alexa
groupStats-class
,
getSigGroups-methods
1 2 3 4 5 6 7 8 9 | ## Not run:
data(GOdata)
data(results.tGO)
showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 5, useInfo = 'all')
printGraph(GOdata, resultFisher, firstSigNodes = 5, fn.prefix = "sampleFile",
useInfo = "all", pdfSW = TRUE)
## End(Not run)
|
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