emapplot_cluster: emapplot_cluster

In enrichplot: Visualization of Functional Enrichment Result

Description

Functional grouping network diagram for enrichment result of over-representation test or gene set enrichment analysis

Usage

emapplot_cluster(
  x,
  showCategory = nrow(x),
  color = "p.adjust",
  label_format = 30,
  ...
)

## S4 method for signature 'enrichResult'
emapplot_cluster(
  x,
  showCategory = 30,
  color = "p.adjust",
  label_format = 30,
  ...
)

## S4 method for signature 'gseaResult'
emapplot_cluster(
  x,
  showCategory = 30,
  color = "p.adjust",
  label_format = 30,
  ...
)

## S4 method for signature 'compareClusterResult'
emapplot_cluster(
  x,
  showCategory = nrow(x),
  color = "p.adjust",
  label_format = 30,
  ...
)

emapplot_cluster.enrichResult(
  x,
  showCategory = 30,
  color = "p.adjust",
  cex_line = 1,
  with_edge = TRUE,
  nWords = 4,
  nCluster = NULL,
  split = NULL,
  min_edge = 0.2,
  cex_label_group = 1,
  label_style = "shadowtext",
  group_legend = FALSE,
  cex_category = 1,
  label_format = 30,
  repel = FALSE,
  ...
)

emapplot_cluster.compareClusterResult(
  x,
  showCategory = 30,
  color = "p.adjust",
  cex_line = 1,
  with_edge = TRUE,
  nWords = 4,
  nCluster = NULL,
  split = NULL,
  min_edge = 0.2,
  cex_label_group = 1,
  pie = "equal",
  legend_n = 5,
  cex_category = 1,
  label_style = "shadowtext",
  group_legend = FALSE,
  label_format = 30,
  repel = FALSE,
  ...
)

Arguments

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
label_format	a numeric value sets wrap length, alternatively a custom function to format axis labels.
...	Additional parameters used to set the position of the group label. When the parameter repel is set to TRUE, additional parameters will take effect. additional parameters can refer the following parameters. force Force of repulsion between overlapping text labels. Defaults to 1. nudge_x, nudge_y Horizontal and vertical adjustments to nudge the starting position of each text label. direction "both", "x", or "y" – direction in which to adjust position of labels.
cex_line	scale of line width
with_edge	if TRUE, draw the edges of the network diagram
nWords	the number of words in the cluster tags
nCluster	the number of clusters
split	separate result by 'category' variable
min_edge	minimum percentage of overlap genes to display the edge, should between 0 and 1, default value is 0.2
cex_label_group	scale of group labels size
label_style	one of "shadowtext" and "ggforce"
group_legend	If TRUE, the grouping legend will be displayed. The default is FALSE
cex_category	number indicating the amount by which plotting category nodes should be scaled relative to the default.
repel	whether to correct the position of the label. Defaults to FALSE.
pie	proportion of clusters in the pie chart, one of 'equal' (default) or 'Count'
legend_n	number of circle in legend

Details

This function visualizes gene sets as a grouped network (i.e. enrichment map). Gene sets with high similarity tend to cluster together, making it easier for interpretation.

Value

ggplot object

Examples

## Not run: 
    library(clusterProfiler)
    library(org.Hs.eg.db)
    library(enrichplot)
    library(GOSemSim)
    library(DOSE)
    data(geneList)
    gene <- names(geneList)[abs(geneList) > 2]
    ego <- enrichGO(gene  = gene,
        universe      = names(geneList),
        OrgDb         = org.Hs.eg.db,
        ont           = "CC",
        pAdjustMethod = "BH",
        pvalueCutoff  = 0.01,
        qvalueCutoff  = 0.05,
        readable      = TRUE)
    d <- godata('org.Hs.eg.db', ont="BP")
    ego2 <- pairwise_termsim(ego, method = "Wang", semData = d)
    emapplot_cluster(ego2, showCategory = 80)
   
## End(Not run)

enrichplot documentation built on Jan. 30, 2021, 2:01 a.m.