dotplot: dotplot

In YuLab-SMU/enrichplot: Visualization of Functional Enrichment Result

dotplot

Description

dotplot for enrichment result

Usage

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,
  ...
)

## S4 method for signature 'enrichResultList'
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 'gseaResultList'
dotplot(
  object,
  x = "GeneRatio",
  color = "p.adjust",
  showCategory = 10,
  size = NULL,
  split = NULL,
  font.size = 12,
  title = "",
  orderBy = "x",
  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,
  facet = NULL,
  strip_width = 15
)

Arguments

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	apply ‘showCategory' to each category specified by the ’split', e.g., "ONTOLOGY", "category" and "intersect". Default is NULL and do nothing
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
facet	apply 'facet_grid' to the plot by specified variable, e.g., "ONTOLOGY", "category" and "intersect".
strip_width	width of strip text, a.k.a facet label.

Value

plot

Author(s)

Guangchuang Yu

Examples

## 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)

YuLab-SMU/enrichplot documentation built on Dec. 18, 2024, 11:52 p.m.