emapplot
Enrichment Map for enrichment result of over-representation test or gene set enrichment analysis
emapplot(x, showCategory = 30, color = "p.adjust", layout = "kk", ...) ## S4 method for signature 'enrichResult' emapplot(x, showCategory = 30, color = "p.adjust", layout = "nicely", ...) ## S4 method for signature 'gseaResult' emapplot(x, showCategory = 30, color = "p.adjust", layout = "nicely", ...) ## S4 method for signature 'compareClusterResult' emapplot(x, showCategory = 30, color = "p.adjust", layout = "nicely", ...) emapplot.enrichResult( x, showCategory = 30, color = "p.adjust", layout = "nicely", node_scale = NULL, line_scale = NULL, min_edge = 0.2, node_label_size = NULL, cex_label_category = 1, cex_category = NULL, cex_line = NULL ) emapplot.compareClusterResult( x, showCategory = 30, color = "p.adjust", layout = "nicely", split = NULL, pie = "equal", legend_n = 5, cex_category = NULL, pie_scale = NULL, cex_line = 1, min_edge = 0.2, cex_label_category = 1, node_label_size = NULL )
x |
enrichment result. |
showCategory |
number of enriched terms to display |
color |
variable that used to color enriched terms, e.g. pvalue, p.adjust or qvalue |
layout |
layout of the map |
... |
additional parameters |
node_scale |
scale of node, this parameter has been changed to cex_category |
line_scale |
scale of line width, this parameter has been changed to cex_line |
min_edge |
minimum percentage of overlap genes to display the edge, should between 0 and 1, default value is 0.2 |
node_label_size |
size of node label, this parameter has been changed to cex_label_category |
cex_label_category |
scale of category node label size |
cex_category |
number indicating the amount by which plotting category nodes should be scaled relative to the default. |
cex_line |
scale of line width |
split |
separate result by 'category' variable |
pie |
proportion of clusters in the pie chart, one of 'equal' (default) or 'Count' |
legend_n |
number of circle in legend |
pie_scale |
scale of pie chart or point, this parameter has been changed to "node_scale" |
This function visualizes gene sets as a network (i.e. enrichment map). Mutually overlapping gene sets tend to cluster together, making it easier for interpretation.
ggplot object
Guangchuang Yu
library(DOSE) data(geneList) de <- names(geneList)[1:100] x <- enrichDO(de) x2 <- pairwise_termsim(x) emapplot(x2)
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