Plots table of enrichment graphs using ggplot and gridExtra.
Plots table of enrichment graphs using ggplot and gridExtra.
plotGseaTable( pathways, stats, fgseaRes, gseaParam = 1, colwidths = c(5, 3, 0.8, 1.2, 1.2), render = TRUE )
pathways |
Pathways to plot table, as in 'fgsea' function. |
stats |
Gene-level stats, as in 'fgsea' function. |
fgseaRes |
Table with fgsea results. |
gseaParam |
GSEA-like parameter. Adjusts displayed statistic values, values closer to 0 flatten plots. Default = 1, value of 0.5 is a good choice too. |
colwidths |
Vector of five elements corresponding to column width for grid.arrange. If column width is set to zero, the column is not drawn. |
render |
If true, the plot is rendered to the current device. Otherwise, the grob is returned. Default is true. |
TableGrob object returned by grid.arrange.
data(examplePathways)
data(exampleRanks)
fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000,
minSize=15, maxSize=100)
topPathways <- fgseaRes[head(order(pval), n=15)][order(NES), pathway]
## Not run:
plotGseaTable(examplePathways[topPathways], exampleRanks,
fgseaRes, gseaParam=0.5)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.