Using one of the network building algorithms, cluster initial network into individual protein complexes.
Usage
X.plot.network(
data = NULL,
scores.col = NA,
standard.set = NULL,
labels.col = NA,
annotation = NULL,
design.params = list(),
export.destination = ".",
network.name = "PPIN",
network.collection = "PPINs",
cytoscape.path = NA,
cytoscape.waittime = 40
)Arguments
- data
Data frame with pair-wise interactions (columns 'protein1' and 'protein2') and a column with probabilities from the ML model.
- scores.col
Character string: Name of the columns with prediction values.
- standard.set
Data frame with columns protein1, protein2 and another column with labels.
- labels.col
Character string: Name of the columns with labels.
- annotation
Data frame with column 'id' with protein IDs and any other annotation columns.
- design.params
List of lines of pieces of code to set up the design of the network plot.
- export.destination
Folder where the files will be saved. Default is the current directory.
- network.name
Title of the network in Cytoscape.
- network.collection
Collection of the network in Cytoscape.
- cytoscape.path
Path to Cytoscape executable file. If not given, the program will try to find it, which may take a long time.
- cytoscape.waittime
Integer: How long should the program wait for the cytoscape to initiate.
Examples
design=list('setNodeShapeDefault("ELLIPSE")','setNodeColorDefault("#5A5A5A")','lockNodeDimensions(TRUE)','setNodeLabelOpacityDefault(1)','setEdgeColorMapping(table.column="complex",list("1","0"), list("#00FF00","#FF0000"),mapping.type="d")','setEdgeLineWidthMapping(mapping.type="c",table.column="pred", widths=c(1,20))')
X.plot.network(final_data,scores.col="score",standard.set=GS,labels.col="complex",annotation=plasmoDB_data%>%rename(protein=Accession),
design.params=design, network.name="MAPX_network", cytoscape.path="C://Program Files/Cytoscape_v3.9.1/Cytoscape.exe")
#> Error: object 'final_data' not found