emapplot | R Documentation |
Enrichment Map for enrichment result of over-representation test or gene set enrichment analysis
emapplot(x, ...)
## S4 method for signature 'enrichResult'
emapplot(x, showCategory = 30, ...)
## S4 method for signature 'gseaResult'
emapplot(x, showCategory = 30, ...)
## S4 method for signature 'compareClusterResult'
emapplot(x, showCategory = 30, ...)
emapplot.enrichResult(
x,
showCategory = 30,
layout = NULL,
coords = NULL,
color = "p.adjust",
min_edge = 0.2,
cex_label_category = 1,
cex_category = 1,
cex_line = 1,
shadowtext = TRUE,
label_style = "shadowtext",
repel = FALSE,
node_label = "category",
with_edge = TRUE,
group_category = FALSE,
group_legend = FALSE,
cex_label_group = 1,
nWords = 4,
label_format = 30,
clusterFunction = stats::kmeans,
nCluster = NULL,
layout.params = list(layout = NULL, coords = NULL),
edge.params = list(show = TRUE, min = 0.2),
cex.params = list(category_node = 1, category_label = 1, line = 1),
hilight.params = list(category = NULL, alpha_hilight = 1, alpha_no_hilight = 0.3),
cluster.params = list(cluster = FALSE, method = stats::kmeans, n = NULL, legend =
FALSE, label_style = "shadowtext", label_words_n = 4, label_format = 30),
...
)
emapplot.compareClusterResult(
x,
showCategory = 30,
layout = NULL,
coords = NULL,
split = NULL,
pie = "equal",
legend_n = 5,
cex_category = 1,
cex_line = 1,
min_edge = 0.2,
cex_label_category = 1,
shadowtext = TRUE,
with_edge = TRUE,
group_category = FALSE,
label_format = 30,
group_legend = FALSE,
node_label = "category",
label_style = "shadowtext",
repel = FALSE,
cex_label_group = 1,
nWords = 4,
clusterFunction = stats::kmeans,
nCluster = NULL,
cex_pie2axis = 1,
pie.params = list(pie = "equal", legend_n = 5),
layout.params = list(layout = NULL, coords = NULL),
edge.params = list(show = TRUE, min = 0.2),
cluster.params = list(cluster = FALSE, method = stats::kmeans, n = NULL, legend =
FALSE, label_style = "shadowtext", label_words_n = 4, label_format = 30),
cex.params = list(category_node = 1, category_label = 1, line = 1, pie2axis = 1,
label_group = 1),
hilight.params = list(category = NULL, alpha_hilight = 1, alpha_no_hilight = 0.3),
...
)
x |
Enrichment result. |
... |
additional parameters additional parameters can refer the following parameters.
|
showCategory |
A number or a vector of terms. If it is a number, the first n terms will be displayed. If it is a vector of terms, the selected terms will be displayed. |
layout |
Layout of the map, e.g. 'star', 'circle', 'gem', 'dh', 'graphopt', 'grid', 'mds', 'randomly', 'fr', 'kk', 'drl' or 'lgl'. Will be removed in the next version. Will be removed in the next version. |
coords |
a data.frame with two columns: 'x' for X-axis coordinate and 'y' for Y-axis coordinate. Will be removed in the next version. |
color |
Variable that used to color enriched terms, e.g. 'pvalue', 'p.adjust' or 'qvalue'. |
min_edge |
The minimum similarity threshold for whether two nodes are connected, should between 0 and 1, default value is 0.2. Will be removed in the next version. |
cex_label_category |
Scale of category node label size. Will be removed in the next version. |
cex_category |
Number indicating the amount by which plotting category nodes should be scaled relative to the default. Will be removed in the next version. |
cex_line |
Scale of line width. Will be removed in the next version. |
shadowtext |
a logical value, whether to use shadow font. |
label_style |
style of group label, one of "shadowtext" and "ggforce". Will be removed in the next version. |
repel |
whether to correct the position of the label. Defaults to FALSE. |
node_label |
Select which labels to be displayed, one of 'category', 'group', 'all' and 'none'. |
with_edge |
Logical, if TRUE, draw the edges of the network diagram. Will be removed in the next version. |
group_category |
a logical, if TRUE, group the category. Will be removed in the next version. |
group_legend |
Logical, if TRUE, the grouping legend will be displayed. The default is FALSE. Will be removed in the next version. |
cex_label_group |
Numeric, scale of group labels size, the default value is 1. Will be removed in the next version. |
nWords |
Numeric, the number of words in the cluster tags, the default value is 4. Will be removed in the next version. |
label_format |
a numeric value sets wrap length, alternatively a custom function to format axis labels. Will be removed in the next version. |
clusterFunction |
function of Clustering method, such as stats::kmeans(the default), cluster::clara, cluster::fanny or cluster::pam. Will be removed in the next version. |
nCluster |
Numeric, the number of clusters, the default value is square root of the number of nodes. Will be removed in the next version. |
layout.params |
list, the parameters to control the layout. see the layout.params in the following. layout.params control the attributes of layout, it can be referred to the following parameters:
|
edge.params |
list, the parameters to control the edge. see the edge.params in the following. edge.params control the attributes of edge, it can be referred to the following parameters:
|
cex.params |
list, the parameters to control the edge. see the cex.params in the following. cex.params control the attributes of edge, it can be referred to the following parameters:
|
hilight.params |
list, the parameters to control the attributes of highlighted nodes and edges. see the hilight.params in the following. hilight.params control the attributes of highlight, it can be referred to the following parameters:
|
cluster.params |
list, the parameters to control the attributes of highlighted nodes and edges. see the cluster.params in the following. cluster.params control the attributes of highlight, it can be referred to the following parameters:
|
split |
separate result by 'category' variable |
pie |
proportion of clusters in the pie chart, one of 'equal' (default) and 'Count' Will be removed in the next version. |
legend_n |
number of circle in legend Will be removed in the next version. |
cex_pie2axis |
It is used to adjust the relative size of the pie chart on the coordinate axis, the default value is 1. Will be removed in the next version. |
pie.params |
list, the parameters to control the attributes of pie nodes. see the pie.params in the following. pie.params control the attributes of pie nodes, it can be referred to the following parameters:
|
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. When the similarity between terms meets a certain threshold (default is 0.2, adjusted by parameter 'min_edge'), there will be edges between terms. The stronger the similarity, the shorter and thicker the edges. The similarity between terms is obtained by function 'pairwise_termsim', the details of similarity calculation can be found in its documentation: pairwise_termsim.
ggplot object
Guangchuang Yu
## Not run:
library(DOSE)
data(geneList)
de <- names(geneList)[1:100]
x <- enrichDO(de)
x2 <- pairwise_termsim(x)
emapplot(x2)
# use `layout` to change the layout of map
emapplot(x2, layout = "star")
# use `showCategory` to select the displayed terms. It can be a number of a vector of terms.
emapplot(x2, showCategory = 10)
categorys <- c("pre-malignant neoplasm", "intestinal disease",
"breast ductal carcinoma")
emapplot(x2, showCategory = categorys)
# It can also graph compareClusterResult
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)
emapplot(xx2)
## End(Not run)
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