dotplot {enrichplot} | R Documentation |
dotplot for enrichment result
dotplot(object, ...) ## S4 method for signature 'enrichResult' dotplot( object, x = "GeneRatio", color = "p.adjust", showCategory = 10, size = NULL, split = NULL, font.size = 12, title = "", orderBy = "x", label_format = 30, ... ) ## S4 method for signature 'gseaResult' dotplot( object, x = "GeneRatio", color = "p.adjust", showCategory = 10, size = NULL, split = NULL, font.size = 12, title = "", orderBy = "x", label_format = 30, ... ) ## S4 method for signature 'compareClusterResult' dotplot( object, x = "Cluster", color = "p.adjust", showCategory = 5, split = NULL, font.size = 12, title = "", by = "geneRatio", size = NULL, includeAll = TRUE, label_format = 30, ... ) dotplot.enrichResult( object, x = "geneRatio", color = "p.adjust", showCategory = 10, size = NULL, split = NULL, font.size = 12, title = "", orderBy = "x", label_format = 30, decreasing = TRUE ) dotplot.compareClusterResult( object, x = "Cluster", colorBy = "p.adjust", showCategory = 5, by = "geneRatio", size = "geneRatio", split = NULL, includeAll = TRUE, font.size = 12, title = "", label_format = 30, group = FALSE, shape = FALSE )
object |
compareClusterResult object |
... |
additional parameters |
x |
variable for x-axis, one of 'GeneRatio' and 'Count' |
color |
variable that used to color enriched terms, e.g. 'pvalue', 'p.adjust' or 'qvalue' |
showCategory |
A number or a list of terms. If it is a number, the first n terms will be displayed. If it is a list of terms, the selected terms will be displayed. |
size |
variable that used to scale the sizes of categories, one of "geneRatio", "Percentage" and "count" |
split |
ONTOLOGY or NULL |
font.size |
font size |
title |
figure title |
orderBy |
The order of the Y-axis |
label_format |
a numeric value sets wrap length, alternatively a custom function to format axis labels. by default wraps names longer that 30 characters |
by |
one of "geneRatio", "Percentage" and "count" |
includeAll |
logical |
decreasing |
logical. Should the orderBy order be increasing or decreasing? |
colorBy |
variable that used to color enriched terms, e.g. 'pvalue', 'p.adjust' or 'qvalue' |
group |
a logical value, whether to connect the nodes of the same group with wires. |
shape |
a logical value, whether to use nodes of different shapes to distinguish the group it belongs to |
plot
guangchuang yu
## Not run: library(DOSE) data(geneList) de <- names(geneList)[1:100] x <- enrichDO(de) dotplot(x) # use `showCategory` to select the displayed terms. It can be a number of a vector of terms. dotplot(x, showCategory = 10) categorys <- c("pre-malignant neoplasm", "intestinal disease", "breast ductal carcinoma", "non-small cell lung carcinoma") dotplot(x, showCategory = categorys) # It can also graph compareClusterResult data(gcSample) library(clusterProfiler) library(DOSE) library(org.Hs.eg.db) data(gcSample) xx <- compareCluster(gcSample, fun="enrichGO", OrgDb="org.Hs.eg.db") xx2 <- pairwise_termsim(xx) library(ggstar) dotplot(xx2) dotplot(xx2, shape = TRUE) dotplot(xx2, group = TRUE) dotplot(xx2, x = "GeneRatio", group = TRUE, size = "count") ## End(Not run)