How to use network.r to draw Network Diagram in R language
This article mainly explains "how to draw a network diagram with network.r in R language". Interested friends may wish to have a look. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn how to draw a network diagram with network.r in R language.
Network.r draws the network graph, the edge weight information determines the thickness of the edges in the network, the degree of the node determines the node size, fills the node color according to the node category, extracts the largest subgraph of the network, outputs the nodes that constitute the largest subgraph and draws the subgraph network.
Usage: Rscript network.r-husage: network.r [- h]-e filepath-v filepath-f from-t to-w weight-g group [--isolated] [- l style] [--label.node] [--sub_label.node] [- o path] [- n prefix] [- H number] [- W number] network plot: https://www..com/article/1531optional arguments:-h -- help show this help message and exit-e filepath,-- edge filepath input the edge information of network, [required]-v filepath,-- vertex filepath input the vertex information of network, [required]-f from,-- from from the name of the start gene column [required]-t to,-- to to the name of the end gene column [required]-w weight -- combined_score weight the name of the edge weight column [required]-- g group,-- group group input group id in vertex file, can set multi groups [required]-- isolated delete isolated vertex [optional, default: False]-l style,-- layout style set Network display style,c ('star',' circle' 'gem',' dh', 'graphopt',' grid', 'mds',' randomly', 'fr',' kk', 'drl',' lgl'), [default fr]-- label.node show node name [optional, default: TRUE]-- sub_label.node show node name of sub-network [optional Default: TRUE]-o path,-- outdir path output file directory [default cwd]-n prefix,-- name prefix out file name prefix [default demo]-H number,-- height number the height of pic inches [default 12]-W number -- width number the width of pic inches [default 12] parameter description:
The edge information file path of the-e network graph, which contains the start node, the end node and the weight information of the edge.
From
To
Combined_score
FromGeneName
ToGeneName
9606.ENSP00000011653
9606.ENSP00000046794
nine hundred and fifty nine
CD4
LCP2
9606.ENSP00000061240
9606.ENSP00000204604
nine hundred and fifty two
TLL1
CHRD
9606.ENSP00000172229
9606.ENSP00000228945
nine hundred and forty five
NGFR
ARHGDIB
-v Node information file path in the network, which contains node (node name corresponds to start node name and end node name in the edge information file) and node category information
Gene
Regulate
CD4
UpTLL1
UpARHGDIB
Up
-f the starting node column name in the edge information file
-t end node column name in the edge information file
-w edge weight column name in edge information file
-g Node category column name in the node information file
-I whether orphan nodes are hidden in the network diagram. They are not hidden by default.
-L whether to mark the node name of the complete network, the default dimension
-S whether to mark the name of the node in the largest subgraph. Default annotation
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