plotMsigNetwork {vissE} | R Documentation |
Plots a network of gene set overlap with overlap computed using the
computeMsigOverlap()
and a graph created using computeMsigNetwork()
.
plotMsigNetwork( ig, markGroups = NULL, genesetStat = NULL, nodeSF = 1, edgeSF = 1, lytFunc = igraph::layout_with_graphopt, lytParams = list() )
ig |
an igraph object, containing a network of gene set overlaps
computed using |
markGroups |
a named list, of character vectors or numeric indices specifying node groupings. Each element of the list represent a group and contains a character vector with node names. Up to 12 groups can be visualised in the plot. |
genesetStat |
a numeric, statistic to project onto the nodes. These could be p-values, log fold-changes or gene set score from a singscore-based analysis. |
nodeSF |
a numeric, indicating the scaling factor to apply to node sizes. |
edgeSF |
a numeric, indicating the scaling factor to apply to edge widths. |
lytFunc |
a function, that computes layouts and returns a matrix with 2 columns specifying the x and y coordinates of nodes. Layout functions in the igraph package can be used here. |
lytParams |
a named list, containing additional parameters to be passed on to the layout function. |
a ggplot2 object
data(hgsc) ovlap <- computeMsigOverlap(hgsc) ig <- computeMsigNetwork(ovlap, hgsc) groups <- list('g1' = c(1, 9), 'g2' = c(5, 6)) plotMsigNetwork(ig, markGroups = groups)