vertex.sort: Elucidates the hierarchical structure of a directed network...
In VertexSort: Network Hierarchical Structure and Randomization
Description
Usage
Arguments
Details
Value
Note
Author(s)
References
Examples
Description
The vertex.sort() function applies a network decomposition
algorithm called the Vertex Sort to a directed network (Jothi et
al. 2009) and generates an object of class vertex.sort. The Vertex
Sort algorithm elucidates the hierarchical structure of a directed network
by classifying its nodes into mainly four layers: the Top, Core,
Bottom and Zero layers. For more information on each of these layers
see details below or refer to (Jothi et al. 2009).
Usage
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vertex.sort(edges)
## S3 method for class 'vertex.sort'
print(x, ...)
## S3 method for class 'vertex.sort'
summary(object, ...)
Arguments
edges
a dataframe that contains a symbolic edge list of the graph
to decompose. It should contain two columns listing Actor and
Target nodes, see details below.
x, object
the vertex.sort object of wich details or summary
will be printed.
...
further arguments passed to or from other methods.
Details
The Vertex Sort algorithm is a network decomposition method that
elucidates the network hierarchy (Jothi et al. 2009). It classifies
network nodes into various levels. First, it transforms the directed
network into an acyclic directed graph. Second, it applies the leaf
removal (LR) algorithm on the network and on its transpose. Third, it
merges the results of the two LR applications into a global result, in
which the level of each node is determined by the possibility of a
node to span many levels. Finally, it groups nodes into four
non-overlapping layers: the Top, Core, Bottom and Zero layers. The
Core layer is made of the nodes composing the biggest strongly
connected component of the network and Top and Bottom layers contain
nodes that regulate and are regulated by the Core layer respectively.
Transforming a network from a cyclic to an acyclic graph is achieved
by collapsing each strongly connected component into a super-node.
The print() function prints the details of a vertex.sort object
(i.e. all the elements of the vertex.sort object).
The summary() function prints a summary of a vertex.sort object.
It describes: the sorted graph (i.e. number of nodes, edges, layers and
levels), the graph layers (i.e. number of nodes of type Actors in Top,
Core and Bottom layers and the number of nodes of type Targets), and
the number of excluded and disconnected nodes (i.e. number of excluded
Actor nodes and the number of disconnected Actor and Target nodes).
Value
The vertex.sort() function returns an object of class vertex.sort.
The functions print() and summary() are used to obtain the
details and a summary of the contents of the vertex.sort objet.
An object of class vertex.sort is a list containing the following elements:
graph
a graph of class igraph containing the edges of
the input network to be sorted.
edges
a dataframe containing the network edges
traits
a dataframe listing the network nodes and determining
whether each of them is of type Actor (node with a non-zero
out-degree) or of type Target (a node with a zero out-degree or a node
that does not regulate an Actor node).
actors
a vector containing all Actor nodes.
targets
a vector containing all Target nodes.
top.actors
a vector containing Actor nodes that were classified
in the Top layer.
core.actors
a vector containing Actor nodes that were classified
in the Core layer.
bottom.actors
a vector containing Actor nodes that were
classified in the Bottom layer.
excluded.actors
a vector containing Actor nodes that were
excluded from the classification, because the algorithm was unable to
classify them propertly.
disconnected.actors
a vector containing Actor nodes that were
found to be disconnected from the input graph and hence were not
subject to the Vertex Sort algorithm.
disconnected.targets
a vector containing Target nodes that were
found to be disconnected from the input graph and hence were not
subject to the decomposition algorithm.
levels.no
an integer indicating the number of levels of the
sorted network.
nodes.in.levels
a list enumerating the nodes belonging to each level.
Note
In the article (Jothi et al. 2009), the authors talked about only
three layers (the Top, Core and Bottom layers). However, in the
present package we talk about four layers, the three layers mentioned
by Jothi et al. in addition to the Zero layer corresponding to the
layer containg the target nodes that do not regulate other Actor nodes.
Author(s)
Diala Abd-Rabbo diala.abd.rabbo@gmail.com
References
Jothi, R., Balaj, S., Wuster, A. et al. 2009 Molecular system
biology 5, –294-309.
Examples
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## load the VertexSort library
library(VertexSort)
## load interactions of the kinase-phosphatase network (kp-net)
data("interactions")
## apply the Vertex Sort algorithm
vs_kp_net <- vertex.sort(interactions)
## print the results (the contents of the vertex.sort object)
vs_kp_net
## print a summary of the results
summary(vs_kp_net)
## print levels.no, an element of the vertex.sort object
vs_kp_net$levels.no
Example output
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: snowfall
Loading required package: snow
Call:
vertex.sort(edges = interactions)
graph:
IGRAPH 17429be DN-B 616 1087 --
+ attr: name (v/n), id (v/n), orf (v/c), type (v/c), level (v/n), layer
| (v/c)
+ edges from 17429be (vertex names):
[1] 1->129 1->130 1->131 1->132 2-> 2 2-> 40 2->133 2->134 3->135
[10] 3-> 19 3->136 3->137 3->138 3->139 3->140 3->141 3->142 3->143
[19] 3->144 3->145 3->146 4-> 10 5->147 5->148 5-> 16 5->149 5->150
[28] 5->151 5->152 6->153 6->154 6->119 6->155 7->156 7->157 7->158
[37] 8-> 8 9->147 9->159 9->160 9-> 16 9->149 9->161 9->162 9->163
[46] 9->164 9->165 9->166 9->167 9->151 9->152 9->102 9->168 10->169
[55] 10->170 10->171 10->172 10->173 10->174 10->175 10-> 2 10->176 10->177
+ ... omitted several edges
Top layer:
[1] "YBL056W" "YBL088C" "YBR125C" "YBR136W" "YCR073C" "YCR091W" "YDL006W"
[8] "YDL047W" "YDL079C" "YDL134C" "YDL188C" "YDR075W" "YDR436W" "YDR490C"
[15] "YER075C" "YER089C" "YER133W" "YFL029C" "YHR102W" "YHR135C" "YIL035C"
[22] "YIL113W" "YJL164C" "YJR066W" "YKL166C" "YKL203C" "YLR433C" "YML016C"
[29] "YML057W" "YMR216C" "YNL154C" "YNL307C" "YOL100W" "YOL128C" "YOR061W"
[36] "YOR208W" "YPL031C" "YPL203W"
Core layer:
[1] "YAR019C" "YBL105C" "YBR160W" "YDL017W" "YDR507C" "YFR028C" "YGR092W"
[8] "YHL007C" "YJL128C" "YJL187C" "YKL048C" "YKL101W" "YLR113W" "YLR362W"
[15] "YMR001C" "YMR036C" "YNL298W" "YNR031C" "YPL153C"
Bottom layer:
[1] "YBL016W" "YBR274W" "YDL028C" "YDL101C" "YDL108W" "YDL159W" "YDR283C"
[8] "YDR477W" "YER129W" "YFL033C" "YGL179C" "YGL180W" "YGR040W" "YGR188C"
[15] "YGR262C" "YHR030C" "YHR205W" "YJL095W" "YJL106W" "YJL141C" "YJR059W"
[22] "YKL126W" "YKL139W" "YLR096W" "YLR248W" "YMR104C" "YNL053W" "YNL161W"
[29] "YNL183C" "YNR047W" "YOR231W" "YOR233W" "YPL140C" "YPL209C" "YPR111W"
[36] "YPR161C"
Excluded actors:
[1] "YAL017W" "YBR059C" "YCR079W" "YDL230W" "YDR122W" "YER139C" "YGL059W"
[8] "YGR123C" "YHR004C" "YIL042C" "YIL095W" "YJL165C" "YKL161C" "YLL010C"
[15] "YLL019C" "YLR361C" "YMR139W" "YMR277W" "YNL020C" "YNL222W" "YOL045W"
[22] "YOR090C" "YOR351C" "YPL042C" "YPL204W" "YPR073C"
Disconnected actors:
[1] "YBR097W" "YBR098W" "YDR247W" "YER123W" "YFR014C" "YHR076W" "YKL171W"
[8] "YLR240W"
Disconnected targets:
[1] "YBR109C" "YCR073W-A" "YDL215C" "YDR080W" "YOR125C"
Levels:
$`Level: 9`
[1] "YMR216C"
$`Level: 8-9`
[1] "YNL307C"
$`Level: 8`
[1] "YML016C"
$`Level: 7-9`
[1] "YBL088C"
$`Level: 7-8`
[1] "YDR490C" "YJL164C"
$`Level: 7`
[1] "YIL035C"
$`Level: 6-9`
[1] "YBR125C" "YCR073C" "YDL006W" "YDL134C" "YDL188C" "YDR075W" "YER075C"
[8] "YFL029C" "YHR135C" "YLR433C" "YML057W" "YNL154C" "YOL100W" "YOR208W"
$`Level: 6-8`
[1] "YBR136W"
$`Level: 6-7`
[1] "YKL166C" "YOR061W" "YPL203W"
$`Level: 6`
[1] "YBL056W" "YER089C"
$`Level: 5`
[1] "YAR019C" "YBL105C" "YBR160W" "YDL017W" "YDR507C" "YFR028C" "YGR092W"
[8] "YHL007C" "YJL128C" "YJL187C" "YKL048C" "YKL101W" "YLR113W" "YLR362W"
[15] "YMR001C" "YMR036C" "YNL298W" "YNR031C" "YPL153C"
$`Level: 4-9`
[1] "YDL047W" "YER133W"
$`Level: 4`
[1] "YER129W"
$`Level: 3-9`
[1] "YCR091W" "YJR066W" "YKL203C"
$`Level: 3`
[1] "YDR477W" "YGL179C"
$`Level: 2-9`
[1] "YDL079C" "YDR436W" "YHR102W" "YIL113W" "YOL128C" "YPL031C"
$`Level: 2-4`
[1] "YDL028C" "YJL095W" "YKL126W" "YNR047W"
$`Level: 2`
[1] "YHR205W"
$`Level: 1-9`
[1] "YAL017W" "YBR059C" "YCR079W" "YDL230W" "YDR122W" "YER139C" "YGL059W"
[8] "YGR123C" "YHR004C" "YIL042C" "YIL095W" "YJL165C" "YKL161C" "YLL010C"
[15] "YLL019C" "YLR361C" "YMR139W" "YMR277W" "YNL020C" "YNL222W" "YOL045W"
[22] "YOR090C" "YOR351C" "YPL042C" "YPL204W" "YPR073C"
$`Level: 1-8`
[1] "YDL108W" "YKL139W" "YNL161W" "YNL183C" "YPR161C"
$`Level: 1-7`
[1] "YBR274W" "YMR104C"
$`Level: 1-6`
[1] "YGL180W" "YJL141C"
$`Level: 1-4`
[1] "YDL101C" "YJL106W" "YJR059W" "YLR096W" "YLR248W" "YOR233W" "YPL209C"
[8] "YPR111W"
$`Level: 1-3`
[1] "YBL016W" "YDL159W" "YGR040W" "YGR188C" "YHR030C" "YNL053W" "YOR231W"
[8] "YPL140C"
$`Level: 1-2`
[1] "YDR283C"
$`Level: 1`
[1] "YFL033C" "YGR262C"
$`Level: 0`
[1] "YAL003W" "YAL005C" "YAL019W" "YAL024C" "YAL028W" "YAL031C" "YAL038W"
[8] "YAL040C" "YAL041W" "YAL043C" "YAL047C" "YAR002W" "YAR007C" "YAR014C"
[15] "YBL002W" "YBL003C" "YBL007C" "YBL023C" "YBL032W" "YBL035C" "YBL039C"
[22] "YBL047C" "YBL051C" "YBL054W" "YBL063W" "YBL078C" "YBL084C" "YBL085W"
[29] "YBL097W" "YBL103C" "YBR009C" "YBR010W" "YBR021W" "YBR023C" "YBR028C"
[36] "YBR038W" "YBR060C" "YBR081C" "YBR083W" "YBR102C" "YBR112C" "YBR133C"
[43] "YBR135W" "YBR143C" "YBR156C" "YBR182C" "YBR200W" "YBR202W" "YBR247C"
[50] "YBR260C" "YCL011C" "YCL014W" "YCL024W" "YCL032W" "YCL037C" "YCL051W"
[57] "YCL061C" "YCL063W" "YCR002C" "YCR014C" "YCR053W" "YCR065W" "YCR077C"
[64] "YCR088W" "YDL003W" "YDL005C" "YDL022W" "YDL088C" "YDL089W" "YDL102W"
[71] "YDL106C" "YDL140C" "YDL149W" "YDL161W" "YDL195W" "YDL201W" "YDL220C"
[78] "YDL225W" "YDR001C" "YDR005C" "YDR028C" "YDR043C" "YDR052C" "YDR054C"
[85] "YDR076W" "YDR082W" "YDR097C" "YDR099W" "YDR103W" "YDR113C" "YDR118W"
[92] "YDR130C" "YDR138W" "YDR146C" "YDR162C" "YDR168W" "YDR169C" "YDR172W"
[99] "YDR184C" "YDR207C" "YDR216W" "YDR217C" "YDR223W" "YDR224C" "YDR225W"
[106] "YDR277C" "YDR285W" "YDR293C" "YDR301W" "YDR310C" "YDR325W" "YDR346C"
[113] "YDR348C" "YDR356W" "YDR369C" "YDR379W" "YDR385W" "YDR386W" "YDR388W"
[120] "YDR422C" "YDR432W" "YDR439W" "YDR443C" "YDR451C" "YDR463W" "YDR468C"
[127] "YDR480W" "YDR496C" "YDR499W" "YDR501W" "YEL009C" "YEL032W" "YEL061C"
[134] "YEL062W" "YER016W" "YER020W" "YER027C" "YER028C" "YER032W" "YER040W"
[141] "YER041W" "YER088C" "YER093C" "YER095W" "YER106W" "YER109C" "YER111C"
[148] "YER114C" "YER118C" "YER148W" "YER149C" "YER151C" "YER155C" "YER161C"
[155] "YER167W" "YER169W" "YER174C" "YER177W" "YER178W" "YFL014W" "YFL021W"
[162] "YFR015C" "YFR021W" "YFR027W" "YFR029W" "YFR034C" "YFR040W" "YFR046C"
[169] "YGL003C" "YGL008C" "YGL019W" "YGL035C" "YGL049C" "YGL058W" "YGL073W"
[176] "YGL075C" "YGL086W" "YGL090W" "YGL093W" "YGL113W" "YGL116W" "YGL122C"
[183] "YGL123W" "YGL163C" "YGL175C" "YGL201C" "YGL208W" "YGL253W" "YGR009C"
[190] "YGR035C" "YGR038W" "YGR082W" "YGR086C" "YGR097W" "YGR108W" "YGR113W"
[197] "YGR140W" "YGR184C" "YGR225W" "YGR233C" "YGR252W" "YGR270W" "YHL020C"
[204] "YHL027W" "YHR005C" "YHR014W" "YHR042W" "YHR071W" "YHR079C" "YHR082C"
[211] "YHR084W" "YHR098C" "YHR107C" "YHR118C" "YHR124W" "YHR149C" "YHR152W"
[218] "YHR154W" "YHR158C" "YHR159W" "YHR161C" "YHR164C" "YHR166C" "YHR172W"
[225] "YIL031W" "YIL033C" "YIL050W" "YIL066C" "YIL072W" "YIL101C" "YIL105C"
[232] "YIL106W" "YIL107C" "YIL109C" "YIL112W" "YIL122W" "YIL144W" "YIL149C"
[239] "YIL159W" "YIR006C" "YIR010W" "YIR023W" "YJL013C" "YJL026W" "YJL076W"
[246] "YJL084C" "YJL089W" "YJL092W" "YJL093C" "YJL098W" "YJL129C" "YJL157C"
[253] "YJL194W" "YJR007W" "YJR021C" "YJR033C" "YJR035W" "YJR049C" "YJR053W"
[260] "YJR057W" "YJR060W" "YJR072C" "YJR076C" "YJR083C" "YJR090C" "YJR092W"
[267] "YJR093C" "YJR094C" "YKL022C" "YKL035W" "YKL038W" "YKL042W" "YKL043W"
[274] "YKL052C" "YKL062W" "YKL089W" "YKL108W" "YKL112W" "YKL129C" "YKL159C"
[281] "YKL160W" "YKL178C" "YKL185W" "YKR002W" "YKR028W" "YKR037C" "YKR038C"
[288] "YKR048C" "YKR089C" "YKR090W" "YKR091W" "YKR095W" "YLL003W" "YLL021W"
[295] "YLL043W" "YLR006C" "YLR035C" "YLR045C" "YLR079W" "YLR086W" "YLR102C"
[302] "YLR103C" "YLR127C" "YLR131C" "YLR133W" "YLR138W" "YLR176C" "YLR182W"
[309] "YLR183C" "YLR187W" "YLR190W" "YLR206W" "YLR212C" "YLR219W" "YLR223C"
[316] "YLR258W" "YLR259C" "YLR263W" "YLR265C" "YLR272C" "YLR277C" "YLR288C"
[323] "YLR310C" "YLR314C" "YLR319C" "YLR335W" "YLR350W" "YLR371W" "YLR384C"
[330] "YLR399C" "YLR410W" "YLR425W" "YLR430W" "YLR437C" "YLR442C" "YLR452C"
[337] "YLR457C" "YML007W" "YML010W" "YML027W" "YML034W" "YML055W" "YML058W"
[344] "YML061C" "YML064C" "YML065W" "YML074C" "YML112W" "YML119W" "YMR005W"
[351] "YMR028W" "YMR032W" "YMR037C" "YMR055C" "YMR070W" "YMR109W" "YMR133W"
[358] "YMR153W" "YMR165C" "YMR172W" "YMR183C" "YMR186W" "YMR190C" "YMR205C"
[365] "YMR224C" "YMR232W" "YMR260C" "YMR273C" "YMR280C" "YMR309C" "YMR311C"
[372] "YNL004W" "YNL025C" "YNL027W" "YNL030W" "YNL031C" "YNL042W" "YNL047C"
[379] "YNL058C" "YNL068C" "YNL076W" "YNL088W" "YNL102W" "YNL118C" "YNL121C"
[386] "YNL126W" "YNL131W" "YNL152W" "YNL157W" "YNL167C" "YNL172W" "YNL178W"
[393] "YNL189W" "YNL197C" "YNL225C" "YNL233W" "YNL242W" "YNL243W" "YNL271C"
[400] "YNL272C" "YNL278W" "YNL289W" "YNL309W" "YNL312W" "YNL321W" "YNR009W"
[407] "YNR016C" "YNR052C" "YOL001W" "YOL018C" "YOL026C" "YOL054W" "YOL059W"
[414] "YOL070C" "YOL078W" "YOL083W" "YOL136C" "YOR014W" "YOR018W" "YOR026W"
[421] "YOR028C" "YOR032C" "YOR033C" "YOR047C" "YOR057W" "YOR058C" "YOR066W"
[428] "YOR070C" "YOR083W" "YOR098C" "YOR119C" "YOR127W" "YOR133W" "YOR140W"
[435] "YOR171C" "YOR174W" "YOR178C" "YOR181W" "YOR189W" "YOR195W" "YOR212W"
[442] "YOR217W" "YOR254C" "YOR257W" "YOR276W" "YOR315W" "YOR322C" "YOR324C"
[449] "YOR329C" "YOR347C" "YOR361C" "YOR372C" "YOR373W" "YPL004C" "YPL014W"
[456] "YPL049C" "YPL089C" "YPL115C" "YPL124W" "YPL133C" "YPL155C" "YPL232W"
[463] "YPL240C" "YPL248C" "YPL256C" "YPL267W" "YPL269W" "YPR007C" "YPR010C"
[470] "YPR016C" "YPR018W" "YPR019W" "YPR030W" "YPR040W" "YPR041W" "YPR054W"
[477] "YPR115W" "YPR119W" "YPR141C" "YPR171W" "YPR174C" "YPR175W" "YPR181C"
[484] "YPR185W"
Call:
summary.vertex.sort(object = vs_kp_net)
Graph description:
Nodes no Edges no Layers no Levels no
616 1087 3 9
Layers description:
Top actors no Core actors no Bottom actors no Targets no
38 19 36 484
Excluded and disconnected nodes:
Excluded actors no Disconnected actors no Disconnected targets no
26 8 5
[1] 9
VertexSort documentation built on May 2, 2019, 9:12 a.m.
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Description Usage Arguments Details Value Note Author(s) References Examples
Description
The vertex.sort() function applies a network decomposition
algorithm called the Vertex Sort to a directed network (Jothi et
al. 2009) and generates an object of class vertex.sort. The Vertex
Sort algorithm elucidates the hierarchical structure of a directed network
by classifying its nodes into mainly four layers: the Top, Core,
Bottom and Zero layers. For more information on each of these layers
see details below or refer to (Jothi et al. 2009).
Usage
1 2 3 4 5 | vertex.sort(edges)
## S3 method for class 'vertex.sort'
print(x, ...)
## S3 method for class 'vertex.sort'
summary(object, ...)
|
Arguments
edges |
a dataframe that contains a symbolic edge list of the graph to decompose. It should contain two columns listing Actor and Target nodes, see details below. |
x, object |
the vertex.sort object of wich details or summary will be printed. |
... |
further arguments passed to or from other methods. |
Details
The Vertex Sort algorithm is a network decomposition method that elucidates the network hierarchy (Jothi et al. 2009). It classifies network nodes into various levels. First, it transforms the directed network into an acyclic directed graph. Second, it applies the leaf removal (LR) algorithm on the network and on its transpose. Third, it merges the results of the two LR applications into a global result, in which the level of each node is determined by the possibility of a node to span many levels. Finally, it groups nodes into four non-overlapping layers: the Top, Core, Bottom and Zero layers. The Core layer is made of the nodes composing the biggest strongly connected component of the network and Top and Bottom layers contain nodes that regulate and are regulated by the Core layer respectively. Transforming a network from a cyclic to an acyclic graph is achieved by collapsing each strongly connected component into a super-node.
The print() function prints the details of a vertex.sort object
(i.e. all the elements of the vertex.sort object).
The summary() function prints a summary of a vertex.sort object.
It describes: the sorted graph (i.e. number of nodes, edges, layers and
levels), the graph layers (i.e. number of nodes of type Actors in Top,
Core and Bottom layers and the number of nodes of type Targets), and
the number of excluded and disconnected nodes (i.e. number of excluded
Actor nodes and the number of disconnected Actor and Target nodes).
Value
The vertex.sort() function returns an object of class vertex.sort.
The functions print() and summary() are used to obtain the
details and a summary of the contents of the vertex.sort objet.
An object of class vertex.sort is a list containing the following elements:
graph |
a graph of class |
edges |
a dataframe containing the network edges |
traits |
a dataframe listing the network nodes and determining whether each of them is of type Actor (node with a non-zero out-degree) or of type Target (a node with a zero out-degree or a node that does not regulate an Actor node). |
actors |
a vector containing all Actor nodes. |
targets |
a vector containing all Target nodes. |
top.actors |
a vector containing Actor nodes that were classified in the Top layer. |
core.actors |
a vector containing Actor nodes that were classified in the Core layer. |
bottom.actors |
a vector containing Actor nodes that were classified in the Bottom layer. |
excluded.actors |
a vector containing Actor nodes that were excluded from the classification, because the algorithm was unable to classify them propertly. |
disconnected.actors |
a vector containing Actor nodes that were found to be disconnected from the input graph and hence were not subject to the Vertex Sort algorithm. |
disconnected.targets |
a vector containing Target nodes that were found to be disconnected from the input graph and hence were not subject to the decomposition algorithm. |
levels.no |
an integer indicating the number of levels of the sorted network. |
nodes.in.levels |
a list enumerating the nodes belonging to each level. |
Note
In the article (Jothi et al. 2009), the authors talked about only three layers (the Top, Core and Bottom layers). However, in the present package we talk about four layers, the three layers mentioned by Jothi et al. in addition to the Zero layer corresponding to the layer containg the target nodes that do not regulate other Actor nodes.
Author(s)
Diala Abd-Rabbo diala.abd.rabbo@gmail.com
References
Jothi, R., Balaj, S., Wuster, A. et al. 2009 Molecular system biology 5, –294-309.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## load the VertexSort library
library(VertexSort)
## load interactions of the kinase-phosphatase network (kp-net)
data("interactions")
## apply the Vertex Sort algorithm
vs_kp_net <- vertex.sort(interactions)
## print the results (the contents of the vertex.sort object)
vs_kp_net
## print a summary of the results
summary(vs_kp_net)
## print levels.no, an element of the vertex.sort object
vs_kp_net$levels.no
|
Example output
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: snowfall
Loading required package: snow
Call:
vertex.sort(edges = interactions)
graph:
IGRAPH 17429be DN-B 616 1087 --
+ attr: name (v/n), id (v/n), orf (v/c), type (v/c), level (v/n), layer
| (v/c)
+ edges from 17429be (vertex names):
[1] 1->129 1->130 1->131 1->132 2-> 2 2-> 40 2->133 2->134 3->135
[10] 3-> 19 3->136 3->137 3->138 3->139 3->140 3->141 3->142 3->143
[19] 3->144 3->145 3->146 4-> 10 5->147 5->148 5-> 16 5->149 5->150
[28] 5->151 5->152 6->153 6->154 6->119 6->155 7->156 7->157 7->158
[37] 8-> 8 9->147 9->159 9->160 9-> 16 9->149 9->161 9->162 9->163
[46] 9->164 9->165 9->166 9->167 9->151 9->152 9->102 9->168 10->169
[55] 10->170 10->171 10->172 10->173 10->174 10->175 10-> 2 10->176 10->177
+ ... omitted several edges
Top layer:
[1] "YBL056W" "YBL088C" "YBR125C" "YBR136W" "YCR073C" "YCR091W" "YDL006W"
[8] "YDL047W" "YDL079C" "YDL134C" "YDL188C" "YDR075W" "YDR436W" "YDR490C"
[15] "YER075C" "YER089C" "YER133W" "YFL029C" "YHR102W" "YHR135C" "YIL035C"
[22] "YIL113W" "YJL164C" "YJR066W" "YKL166C" "YKL203C" "YLR433C" "YML016C"
[29] "YML057W" "YMR216C" "YNL154C" "YNL307C" "YOL100W" "YOL128C" "YOR061W"
[36] "YOR208W" "YPL031C" "YPL203W"
Core layer:
[1] "YAR019C" "YBL105C" "YBR160W" "YDL017W" "YDR507C" "YFR028C" "YGR092W"
[8] "YHL007C" "YJL128C" "YJL187C" "YKL048C" "YKL101W" "YLR113W" "YLR362W"
[15] "YMR001C" "YMR036C" "YNL298W" "YNR031C" "YPL153C"
Bottom layer:
[1] "YBL016W" "YBR274W" "YDL028C" "YDL101C" "YDL108W" "YDL159W" "YDR283C"
[8] "YDR477W" "YER129W" "YFL033C" "YGL179C" "YGL180W" "YGR040W" "YGR188C"
[15] "YGR262C" "YHR030C" "YHR205W" "YJL095W" "YJL106W" "YJL141C" "YJR059W"
[22] "YKL126W" "YKL139W" "YLR096W" "YLR248W" "YMR104C" "YNL053W" "YNL161W"
[29] "YNL183C" "YNR047W" "YOR231W" "YOR233W" "YPL140C" "YPL209C" "YPR111W"
[36] "YPR161C"
Excluded actors:
[1] "YAL017W" "YBR059C" "YCR079W" "YDL230W" "YDR122W" "YER139C" "YGL059W"
[8] "YGR123C" "YHR004C" "YIL042C" "YIL095W" "YJL165C" "YKL161C" "YLL010C"
[15] "YLL019C" "YLR361C" "YMR139W" "YMR277W" "YNL020C" "YNL222W" "YOL045W"
[22] "YOR090C" "YOR351C" "YPL042C" "YPL204W" "YPR073C"
Disconnected actors:
[1] "YBR097W" "YBR098W" "YDR247W" "YER123W" "YFR014C" "YHR076W" "YKL171W"
[8] "YLR240W"
Disconnected targets:
[1] "YBR109C" "YCR073W-A" "YDL215C" "YDR080W" "YOR125C"
Levels:
$`Level: 9`
[1] "YMR216C"
$`Level: 8-9`
[1] "YNL307C"
$`Level: 8`
[1] "YML016C"
$`Level: 7-9`
[1] "YBL088C"
$`Level: 7-8`
[1] "YDR490C" "YJL164C"
$`Level: 7`
[1] "YIL035C"
$`Level: 6-9`
[1] "YBR125C" "YCR073C" "YDL006W" "YDL134C" "YDL188C" "YDR075W" "YER075C"
[8] "YFL029C" "YHR135C" "YLR433C" "YML057W" "YNL154C" "YOL100W" "YOR208W"
$`Level: 6-8`
[1] "YBR136W"
$`Level: 6-7`
[1] "YKL166C" "YOR061W" "YPL203W"
$`Level: 6`
[1] "YBL056W" "YER089C"
$`Level: 5`
[1] "YAR019C" "YBL105C" "YBR160W" "YDL017W" "YDR507C" "YFR028C" "YGR092W"
[8] "YHL007C" "YJL128C" "YJL187C" "YKL048C" "YKL101W" "YLR113W" "YLR362W"
[15] "YMR001C" "YMR036C" "YNL298W" "YNR031C" "YPL153C"
$`Level: 4-9`
[1] "YDL047W" "YER133W"
$`Level: 4`
[1] "YER129W"
$`Level: 3-9`
[1] "YCR091W" "YJR066W" "YKL203C"
$`Level: 3`
[1] "YDR477W" "YGL179C"
$`Level: 2-9`
[1] "YDL079C" "YDR436W" "YHR102W" "YIL113W" "YOL128C" "YPL031C"
$`Level: 2-4`
[1] "YDL028C" "YJL095W" "YKL126W" "YNR047W"
$`Level: 2`
[1] "YHR205W"
$`Level: 1-9`
[1] "YAL017W" "YBR059C" "YCR079W" "YDL230W" "YDR122W" "YER139C" "YGL059W"
[8] "YGR123C" "YHR004C" "YIL042C" "YIL095W" "YJL165C" "YKL161C" "YLL010C"
[15] "YLL019C" "YLR361C" "YMR139W" "YMR277W" "YNL020C" "YNL222W" "YOL045W"
[22] "YOR090C" "YOR351C" "YPL042C" "YPL204W" "YPR073C"
$`Level: 1-8`
[1] "YDL108W" "YKL139W" "YNL161W" "YNL183C" "YPR161C"
$`Level: 1-7`
[1] "YBR274W" "YMR104C"
$`Level: 1-6`
[1] "YGL180W" "YJL141C"
$`Level: 1-4`
[1] "YDL101C" "YJL106W" "YJR059W" "YLR096W" "YLR248W" "YOR233W" "YPL209C"
[8] "YPR111W"
$`Level: 1-3`
[1] "YBL016W" "YDL159W" "YGR040W" "YGR188C" "YHR030C" "YNL053W" "YOR231W"
[8] "YPL140C"
$`Level: 1-2`
[1] "YDR283C"
$`Level: 1`
[1] "YFL033C" "YGR262C"
$`Level: 0`
[1] "YAL003W" "YAL005C" "YAL019W" "YAL024C" "YAL028W" "YAL031C" "YAL038W"
[8] "YAL040C" "YAL041W" "YAL043C" "YAL047C" "YAR002W" "YAR007C" "YAR014C"
[15] "YBL002W" "YBL003C" "YBL007C" "YBL023C" "YBL032W" "YBL035C" "YBL039C"
[22] "YBL047C" "YBL051C" "YBL054W" "YBL063W" "YBL078C" "YBL084C" "YBL085W"
[29] "YBL097W" "YBL103C" "YBR009C" "YBR010W" "YBR021W" "YBR023C" "YBR028C"
[36] "YBR038W" "YBR060C" "YBR081C" "YBR083W" "YBR102C" "YBR112C" "YBR133C"
[43] "YBR135W" "YBR143C" "YBR156C" "YBR182C" "YBR200W" "YBR202W" "YBR247C"
[50] "YBR260C" "YCL011C" "YCL014W" "YCL024W" "YCL032W" "YCL037C" "YCL051W"
[57] "YCL061C" "YCL063W" "YCR002C" "YCR014C" "YCR053W" "YCR065W" "YCR077C"
[64] "YCR088W" "YDL003W" "YDL005C" "YDL022W" "YDL088C" "YDL089W" "YDL102W"
[71] "YDL106C" "YDL140C" "YDL149W" "YDL161W" "YDL195W" "YDL201W" "YDL220C"
[78] "YDL225W" "YDR001C" "YDR005C" "YDR028C" "YDR043C" "YDR052C" "YDR054C"
[85] "YDR076W" "YDR082W" "YDR097C" "YDR099W" "YDR103W" "YDR113C" "YDR118W"
[92] "YDR130C" "YDR138W" "YDR146C" "YDR162C" "YDR168W" "YDR169C" "YDR172W"
[99] "YDR184C" "YDR207C" "YDR216W" "YDR217C" "YDR223W" "YDR224C" "YDR225W"
[106] "YDR277C" "YDR285W" "YDR293C" "YDR301W" "YDR310C" "YDR325W" "YDR346C"
[113] "YDR348C" "YDR356W" "YDR369C" "YDR379W" "YDR385W" "YDR386W" "YDR388W"
[120] "YDR422C" "YDR432W" "YDR439W" "YDR443C" "YDR451C" "YDR463W" "YDR468C"
[127] "YDR480W" "YDR496C" "YDR499W" "YDR501W" "YEL009C" "YEL032W" "YEL061C"
[134] "YEL062W" "YER016W" "YER020W" "YER027C" "YER028C" "YER032W" "YER040W"
[141] "YER041W" "YER088C" "YER093C" "YER095W" "YER106W" "YER109C" "YER111C"
[148] "YER114C" "YER118C" "YER148W" "YER149C" "YER151C" "YER155C" "YER161C"
[155] "YER167W" "YER169W" "YER174C" "YER177W" "YER178W" "YFL014W" "YFL021W"
[162] "YFR015C" "YFR021W" "YFR027W" "YFR029W" "YFR034C" "YFR040W" "YFR046C"
[169] "YGL003C" "YGL008C" "YGL019W" "YGL035C" "YGL049C" "YGL058W" "YGL073W"
[176] "YGL075C" "YGL086W" "YGL090W" "YGL093W" "YGL113W" "YGL116W" "YGL122C"
[183] "YGL123W" "YGL163C" "YGL175C" "YGL201C" "YGL208W" "YGL253W" "YGR009C"
[190] "YGR035C" "YGR038W" "YGR082W" "YGR086C" "YGR097W" "YGR108W" "YGR113W"
[197] "YGR140W" "YGR184C" "YGR225W" "YGR233C" "YGR252W" "YGR270W" "YHL020C"
[204] "YHL027W" "YHR005C" "YHR014W" "YHR042W" "YHR071W" "YHR079C" "YHR082C"
[211] "YHR084W" "YHR098C" "YHR107C" "YHR118C" "YHR124W" "YHR149C" "YHR152W"
[218] "YHR154W" "YHR158C" "YHR159W" "YHR161C" "YHR164C" "YHR166C" "YHR172W"
[225] "YIL031W" "YIL033C" "YIL050W" "YIL066C" "YIL072W" "YIL101C" "YIL105C"
[232] "YIL106W" "YIL107C" "YIL109C" "YIL112W" "YIL122W" "YIL144W" "YIL149C"
[239] "YIL159W" "YIR006C" "YIR010W" "YIR023W" "YJL013C" "YJL026W" "YJL076W"
[246] "YJL084C" "YJL089W" "YJL092W" "YJL093C" "YJL098W" "YJL129C" "YJL157C"
[253] "YJL194W" "YJR007W" "YJR021C" "YJR033C" "YJR035W" "YJR049C" "YJR053W"
[260] "YJR057W" "YJR060W" "YJR072C" "YJR076C" "YJR083C" "YJR090C" "YJR092W"
[267] "YJR093C" "YJR094C" "YKL022C" "YKL035W" "YKL038W" "YKL042W" "YKL043W"
[274] "YKL052C" "YKL062W" "YKL089W" "YKL108W" "YKL112W" "YKL129C" "YKL159C"
[281] "YKL160W" "YKL178C" "YKL185W" "YKR002W" "YKR028W" "YKR037C" "YKR038C"
[288] "YKR048C" "YKR089C" "YKR090W" "YKR091W" "YKR095W" "YLL003W" "YLL021W"
[295] "YLL043W" "YLR006C" "YLR035C" "YLR045C" "YLR079W" "YLR086W" "YLR102C"
[302] "YLR103C" "YLR127C" "YLR131C" "YLR133W" "YLR138W" "YLR176C" "YLR182W"
[309] "YLR183C" "YLR187W" "YLR190W" "YLR206W" "YLR212C" "YLR219W" "YLR223C"
[316] "YLR258W" "YLR259C" "YLR263W" "YLR265C" "YLR272C" "YLR277C" "YLR288C"
[323] "YLR310C" "YLR314C" "YLR319C" "YLR335W" "YLR350W" "YLR371W" "YLR384C"
[330] "YLR399C" "YLR410W" "YLR425W" "YLR430W" "YLR437C" "YLR442C" "YLR452C"
[337] "YLR457C" "YML007W" "YML010W" "YML027W" "YML034W" "YML055W" "YML058W"
[344] "YML061C" "YML064C" "YML065W" "YML074C" "YML112W" "YML119W" "YMR005W"
[351] "YMR028W" "YMR032W" "YMR037C" "YMR055C" "YMR070W" "YMR109W" "YMR133W"
[358] "YMR153W" "YMR165C" "YMR172W" "YMR183C" "YMR186W" "YMR190C" "YMR205C"
[365] "YMR224C" "YMR232W" "YMR260C" "YMR273C" "YMR280C" "YMR309C" "YMR311C"
[372] "YNL004W" "YNL025C" "YNL027W" "YNL030W" "YNL031C" "YNL042W" "YNL047C"
[379] "YNL058C" "YNL068C" "YNL076W" "YNL088W" "YNL102W" "YNL118C" "YNL121C"
[386] "YNL126W" "YNL131W" "YNL152W" "YNL157W" "YNL167C" "YNL172W" "YNL178W"
[393] "YNL189W" "YNL197C" "YNL225C" "YNL233W" "YNL242W" "YNL243W" "YNL271C"
[400] "YNL272C" "YNL278W" "YNL289W" "YNL309W" "YNL312W" "YNL321W" "YNR009W"
[407] "YNR016C" "YNR052C" "YOL001W" "YOL018C" "YOL026C" "YOL054W" "YOL059W"
[414] "YOL070C" "YOL078W" "YOL083W" "YOL136C" "YOR014W" "YOR018W" "YOR026W"
[421] "YOR028C" "YOR032C" "YOR033C" "YOR047C" "YOR057W" "YOR058C" "YOR066W"
[428] "YOR070C" "YOR083W" "YOR098C" "YOR119C" "YOR127W" "YOR133W" "YOR140W"
[435] "YOR171C" "YOR174W" "YOR178C" "YOR181W" "YOR189W" "YOR195W" "YOR212W"
[442] "YOR217W" "YOR254C" "YOR257W" "YOR276W" "YOR315W" "YOR322C" "YOR324C"
[449] "YOR329C" "YOR347C" "YOR361C" "YOR372C" "YOR373W" "YPL004C" "YPL014W"
[456] "YPL049C" "YPL089C" "YPL115C" "YPL124W" "YPL133C" "YPL155C" "YPL232W"
[463] "YPL240C" "YPL248C" "YPL256C" "YPL267W" "YPL269W" "YPR007C" "YPR010C"
[470] "YPR016C" "YPR018W" "YPR019W" "YPR030W" "YPR040W" "YPR041W" "YPR054W"
[477] "YPR115W" "YPR119W" "YPR141C" "YPR171W" "YPR174C" "YPR175W" "YPR181C"
[484] "YPR185W"
Call:
summary.vertex.sort(object = vs_kp_net)
Graph description:
Nodes no Edges no Layers no Levels no
616 1087 3 9
Layers description:
Top actors no Core actors no Bottom actors no Targets no
38 19 36 484
Excluded and disconnected nodes:
Excluded actors no Disconnected actors no Disconnected targets no
26 8 5
[1] 9
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