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 = "graphopt", lytParams = list() )
ig |
an igraph object, containing a network of gene set overlaps
computed using |
markGroups |
a named list, of character vectors. 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 named 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 character, specifying the layout to use (see
|
lytParams |
a named list, containing additional parameters needed for
the layout (see |
a ggplot2 object
data(hgsc) ovlap <- computeMsigOverlap(hgsc, thresh = 0.15) ig <- computeMsigNetwork(ovlap, hgsc) groups <- list( 'g1' = c("HALLMARK_HYPOXIA", "HALLMARK_GLYCOLYSIS"), 'g2' = c("HALLMARK_INTERFERON_GAMMA_RESPONSE") ) plotMsigNetwork(ig, markGroups = groups)