Usage
mst.plot(x, layout.function=NULL,colors=NULL,mst.edge.col="white",
vertex.color = "skyblue",tkplot=FALSE,expression=NULL, v.size=FALSE,
e.size=FALSE, mst.e.size=1, edge.col.wt=NULL, v.lab=FALSE,
e.lab=NULL, bg="black",v.lab.cex=0.5, e.lab.cex=0.5,
v.lab.col="blue",lab.dist=0, e.lab.col="blue",
v.sf=c(3,12),e.arrow=.2)
Arguments
x
x
is a graph object, created using the igraph package.
layout.function
layout.function
is a function class. The user can pass his own function to plot the graph. The input function passed to layout.function
should return a 2D matrix of coordinates with rows equal to the number of vertices of the input graph and two columns representing x and y coordinates.
mst.edge.col
This option assigns a color to the edges of the minimum spanning tree of graph 'g'. The default color is black for 'tkplot=TRUE'. If 'tkplot=FALSE' it is white.
colors
colors
is a vector for the edge colors to color the remaining edges of a graph. The remaining edges are colored based on the distance between the nodes connecting them.
vertex.color
vertex.colors
is a vector of colors for the vertices of a graph.
expression
expression
is a numeric vector which represents properties of genes or proteins, e.g., their mean expression values or p-values. If this option is given, the nodes are colored with a range of colors from red to blue (red for low expression, blue for high expression) depending on the expression values.
tkplot
tkplot
is a boolean variable. If it is FALSE, the graph is plotted with the plot function with a black background.
v.size
is a numeric value or a numeric vector which contains values to assign the size of the nodes.
e.size
is a numeric value or a numeric vector which contains values to assign the width of edgesother than the minimum spanning tree edges of the graph.
mst.e.size
is a numeric value which assigns the edge width to the edges of minimum spanning tree of the input graph.
v.lab
is logical value to show vertex labels.
e.lab
is logical value to show edge labels.
bg
is a character value to color the background.
v.lab.cex
is a numerical value to set the font size of the vertex labels.
e.lab.cex
is a numerical value to set the font size of the edge labels.
lab.dist
is a numerical value to adjust the distance of labels from the nodes.
v.lab.col
is a hexadecimal character value to assign colors to the vertex labels.
e.lab.col
is a hexadecimal character value to assign colors to the edge labels.
e.arrow
is a inumerical value to set the arrow width in a directed network.
v.sf
is a 2 dimensional numeric vector, which represents the minimum and maximum limits of the size of vertices. This is used to adjust the vertex size when the v.size
input is a numeric vector.
edge.col.wt
is a vector of numeric values provided for each edge. This is used to color the edges from blue to red from high to low values.
...
...
parameter for other inputs.