Package enrichplot. September 29, 2018
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1 Package enrichplot September 29, 2018 Title Visualization of Functional Enrichment Result Version The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. All the visualization methods are developed based on 'ggplot2' graphics. Depends R (>= 3.4.0) Imports AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2, ggplotify, ggraph, ggridges, GOSemSim, graphics, grdevices, grid, gridetra, igraph, methods, purrr, RColorBrewer, reshape2, stats, UpSetR, utils Suggests clusterprofiler, knitr, org.hs.eg.db, prettydoc VignetteBuilder knitr License Artistic-2.0 URL BugReports biocviews Annotation, GeneSetEnrichment, GO, KEGG, Pathways, Software, Visualization Encoding UTF-8 LazyData true RoygenNote git_url git_branch master git_last_commit f git_last_commit_date Date/Publication Author [aut, cre] (< Maintainer <guangchuangyu@gmail.com> 1
2 2 barplot.enrichresult R topics documented: barplot.enrichresult cnetplot color_palette dotplot emapplot fortify.enrichresult ggtable goplot gseaplot gseaplot gsearank gsinfo heatplot list2graph pmcplot ridgeplot upsetplot Inde 16 barplot.enrichresult barplot barplot of enrichresult ## S3 method for class 'enrichresult' barplot(height, = "Count", color = "p.adjust", showcategory = 8, font.size = 12, title = "",...) height enrichresult object one of Count and GeneRatio color one of pvalue, p.adjust, qvalue showcategory number of categories to show font.size font size title plot title... other parameter, ignored
3 cnetplot 3 Eamples library(dose) data(genelist) de <- names(genelist)[1:100] <- enrichdo(de) barplot() cnetplot cnetplot Gene-Concept Network cnetplot(, showcategory = 5, foldchange = NULL, layout = "kk",...) ## S4 method for signature 'enrichresult' cnetplot(, showcategory = 5, foldchange = NULL, layout = "kk",...) ## S4 method for signature 'gsearesult' cnetplot(, showcategory = 5, foldchange = NULL, layout = "kk",...) cnetplot.enrichresult(, showcategory = 5, foldchange = NULL, layout = "kk", coloredge = FALSE, circular = FALSE, node_label = TRUE,...) enrichment result showcategory number of enriched terms to display foldchange fold Change layout layout of the network... additional parameters coloredge whether coloring edge by enriched terms circular whether using circular layout node_label whether display node label Details plot linkages of genes and enriched concepts (e.g. GO categories, KEGG pathways)
4 4 color_palette Eamples library(dose) data(genelist) de <- names(genelist)[1:100] <- enrichdo(de) cnetplot() color_palette color_palette create color palette for continuous data color_palette(colors) colors colors of length >=2 color vector guangchuang yu Eamples color_palette(c("red", "yellow", "green"))
5 dotplot 5 dotplot dotplot dotplot for enrichment result dotplot(object,...) ## S4 method for signature 'enrichresult' dotplot(object, = "GeneRatio", color = "p.adjust", showcategory = 10, split = NULL, font.size = 12, title = "",...) ## S4 method for signature 'gsearesult' dotplot(object, = "GeneRatio", color = "p.adjust", showcategory = 10, split = NULL, font.size = 12, title = "",...) object input object... additional parameters variable for -ais, one of GeneRatio or Count color variable that used to color enriched terms, e.g. pvalue, p.adjust or qvalue showcategory number of enriched terms to display split separate result by category variable font.size font size title plot title plot guangchuang yu Eamples library(dose) data(genelist) de <- names(genelist)[1:100] <- enrichdo(de) dotplot()
6 6 emapplot emapplot emapplot Enrichment Map for enrichment result of over-representation test or gene set enrichment analysis emapplot(, showcategory = 30, color = "p.adjust", layout = "kk",...) ## S4 method for signature 'enrichresult' emapplot(, showcategory = 30, color = "p.adjust", layout = "kk",...) ## S4 method for signature 'gsearesult' emapplot(, showcategory = 30, color = "p.adjust", layout = "kk",...) emapplot.enrichresult(, showcategory = 30, color = "p.adjust", layout = "kk",...) Details showcategory color layout enrichment result. number of enriched terms to display variable that used to color enriched terms, e.g. pvalue, p.adjust or qvalue layout of the map... additional 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. Eamples library(dose) data(genelist) de <- names(genelist)[1:100] <- enrichdo(de) emapplot()
7 fortify.enrichresult 7 fortify.enrichresult fortify convert enrichresult object for ggplot2 ## S3 method for class 'enrichresult' fortify(model, data, showcategory = 5, by = "Count", order = FALSE, drop = FALSE, split = NULL,...) model enrichresult object data not use here showcategory Category numbers to show by one of Count and GeneRatio order logical drop logical split separate result by split variable... additional parameter data.frame ggtable ggtable plot table ggtable(d, p = NULL) d p data frame to etract color to color rownames(d), optional guangchuang yu
8 8 goplot goplot goplot plot induced GO DAG of significant terms goplot(, showcategory = 10, color = "p.adjust", layout = "sugiyama", geom = "tet",...) ## S4 method for signature 'enrichresult' goplot(, showcategory = 10, color = "p.adjust", layout = "sugiyama", geom = "tet",...) ## S4 method for signature 'gsearesult' goplot(, showcategory = 10, color = "p.adjust", layout = "sugiyama", geom = "tet",...) goplot.enrichresult(, showcategory = 10, color = "p.adjust", layout = "sugiyama", geom = "tet",...) showcategory color layout geom enrichment result. number of enriched terms to display variable that used to color enriched terms, e.g. pvalue, p.adjust or qvalue layout of the map label geom, one of label or tet... additional parameter guangchuang yu
9 gseaplot 9 gseaplot gseaplot visualize analyzing result of GSEA gseaplot(, genesetid, by = "all", title = "",...) ## S4 method for signature 'gsearesult' gseaplot(, genesetid, by = "all", title = "", color = "black", color.line = "green", color.vline = "#FA5860",...) gseaplot.gsearesult(, genesetid, by = "all", title = "", color = "black", color.line = "green", color.vline = "#FA5860",...) genesetid by Details title object of gsea result geneset ID one of "runningscore" or "position" plot title... additional parameters color color.line color.vline color of line segments plotting function for gsearesult ggplot2 object ggplot2 object Eamples library(dose) data(genelist) <- gsedo(genelist) gseaplot(, genesetid=1) color of running enrichment score line color of vertical line which indicating the maimum/minimal running enrichment score
10 10 gsearank gseaplot2 gseaplot2 GSEA plot that mimic the plot generated by broad institute s GSEA software gseaplot2(, genesetid, title = "", color = "green", base_size = 11, rel_heights = c(1.5, 0.5, 1), subplots = 1:3, pvalue_table = FALSE, ES_geom = "line") genesetid title color base_size rel_heights subplots pvalue_table ES_geom gsearesult object gene set ID plot title color of running enrichment score line base font size relative heights of subplots which subplots to be displayed whether add pvalue table geom for plotting running enrichment score, one of line or dot plot gsearank gsearank plot ranked list of genes with running enrichment score as bar height gsearank(, genesetid, title = "")
11 gsinfo 11 genesetid title gsearesult object gene set ID plot title gsinfo gsinfo etract gsea result of selected geneset gsinfo(object, genesetid) object genesetid gsearesult object gene set ID data.frame
12 12 heatplot heatplot heatplot heatmap like plot for functional classification heatplot(, showcategory = 30, foldchange = NULL) ## S4 method for signature 'enrichresult' heatplot(, showcategory = 30, foldchange = NULL) ## S4 method for signature 'gsearesult' heatplot(, showcategory = 30, foldchange = NULL) heatplot.enrichresult(, showcategory = 30, foldchange = NULL) showcategory foldchange enrichment result. number of enriched terms to display fold Change guangchuang yu Eamples library(dose) data(genelist) de <- names(genelist)[1:100] <- enrichdo(de) heatplot()
13 list2graph 13 list2graph convert gene IDs to igraph object convert a list of gene IDs to igraph object. list2graph(inputlist) inputlist a list of gene IDs a igraph object. pmcplot pmcplot PubMed Central Trend plot pmcplot(query, period, proportion = TRUE) query period proportion query terms period of query in the unit of year If TRUE, use query_hits/all_hits, otherwise use query_hits guangchuang yu
14 14 ridgeplot ridgeplot ridgeplot ridgeline plot for GSEA result ridgeplot(, showcategory = 30, fill = "p.adjust", core_enrichment = TRUE) ## S4 method for signature 'gsearesult' ridgeplot(, showcategory = 30, fill = "p.adjust", core_enrichment = TRUE) ridgeplot.gsearesult(, showcategory = 30, fill = "p.adjust", core_enrichment = TRUE) showcategory gsearesult object number of categories for plotting fill one of "pvalue", "p.adjust", "qvalue" core_enrichment whether only using core_enriched genes Eamples library(dose) data(genelist) <- gsedo(genelist) ridgeplot()
15 upsetplot 15 upsetplot upsetplot method upsetplot method generics upsetplot upsetplot(,...) ## S4 method for signature 'enrichresult' upsetplot(, n = 10,...) object... additional parameters n plot Eamples require(dose) data(genelist) de=names(genelist)[1:100] <- enrichdo(de) upsetplot(, 8) number of categories to be plotted
16 Inde barplot.enrichresult, 2 cnetplot, 3 cnetplot,enrichresult-method (cnetplot), 3 cnetplot,gsearesult-method (cnetplot), 3 cnetplot.enrichresult (cnetplot), 3 color_palette, 4 dotplot, 5 dotplot,enrichresult-method (dotplot), 5 dotplot,gsearesult-method (dotplot), 5 ridgeplot,gsearesult-method (ridgeplot), 14 ridgeplot.gsearesult (ridgeplot), 14 upsetplot, 15 upsetplot,enrichresult,any-method (upsetplot), 15 upsetplot,enrichresult-method (upsetplot), 15 emapplot, 6 emapplot,enrichresult-method (emapplot), 6 emapplot,gsearesult-method (emapplot), 6 emapplot.enrichresult (emapplot), 6 fortify.enrichresult, 7 ggtable, 7 goplot, 8 goplot,enrichresult-method (goplot), 8 goplot,gsearesult-method (goplot), 8 goplot.enrichresult (goplot), 8 gseaplot, 9 gseaplot,gsearesult-method (gseaplot), 9 gseaplot.gsearesult (gseaplot), 9 gseaplot2, 10 gsearank, 10 gsinfo, 11 heatplot, 12 heatplot,enrichresult-method (heatplot), 12 heatplot,gsearesult-method (heatplot), 12 heatplot.enrichresult (heatplot), 12 list2graph, 13 pmcplot, 13 ridgeplot, 14 16
Package clusterprofiler
Type Package Package clusterprofiler December 22, 2018 Title statistical analysis and visualization of functional profiles for genes and gene clusters Version 3.10.1 Maintainer
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Using clusterprofiler to identify and compare functional profiles of gene lists
Using clusterprofiler to identify and compare functional profiles of gene lists Guangchuang Yu School of Biological Sciences The University of Hong Kong, Hong Kong SAR, China email: gcyu@connect.hku.hk
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Title Reproduce figures in IHW paper Version 1.10.0 Package IHWpaper March 7, 2019 This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885)
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Type Package Package dupradar July 12, 2018 Title Assessment of duplication rates in RNA-Seq datasets Version 1.10.0 Date 2015-09-26 Author Sergi Sayols , Holger Klein
Package Numero. November 24, 2018
Package Numero November 24, 2018 Type Package Title Statistical Framework to Define Subgroups in Complex Datasets Version 1.1.1 Date 2018-11-21 Author Song Gao [aut], Stefan Mutter [aut], Aaron E. Casey
Package ggmosaic. February 9, 2017
Title Mosaic Plots in the 'ggplot2' Framework Version 0.1.2 Package ggmosaic February 9, 2017 Mosaic plots in the 'ggplot2' framework. Mosaic plot functionality is provided in a single 'ggplot2' layer
Package smoothr. April 4, 2018
Type Package Title Smooth and Tidy Spatial Features Version 0.1.0 Package smoothr April 4, 2018 Tools for smoothing and tidying spatial features (i.e. lines and polygons) to make them more aesthetically
Package mschart. April 20, Type Package
Type Package Package mschart April 20, 2018 Title Chart Generation for 'Microsoft Word' and 'Microsoft PowerPoint' Documents Version 0.2.3 Create native charts for 'Microsoft PowerPoint' and 'Microsoft
Package MSstatsQC. R topics documented: November 3, Version Type Package
Version 2.0.0 Type Package Package MSstatsQC November 3, 2018 Title Longitudinal system suitability monitoring and quality control for proteomic experiments MSstatsQC is an R package which provides longitudinal
Package BDMMAcorrect
Type Package Package BDMMAcorrect March 6, 2019 Title Meta-analysis for the metagenomic read counts data from different cohorts Version 1.0.1 Author ZHENWEI DAI Maintainer ZHENWEI
Package cowplot. March 6, 2016
Package cowplot March 6, 2016 Title Streamlined Plot Theme and Plot Annotations for 'ggplot2' Version 0.6.1 Some helpful extensions and modifications to the 'ggplot2' library. In particular, this package
Package Glimma. June 29, 2018
Type Package Title Interactive HTML graphics Version 1.8.2 Date 2016-12-21 Package Glimma June 29, 2018 This package generates interactive visualisations for analysis of RNA-sequencing data using output
Package textrank. December 18, 2017
Package textrank December 18, 2017 Type Package Title Summarize Text by Ranking Sentences and Finding Keywords Version 0.2.0 Maintainer Jan Wijffels Author Jan Wijffels [aut, cre,
Package GARS. March 17, 2019
Type Package Date 2018-10-09 Package GARS March 17, 2019 Title GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets Version 1.2.0 Author
Package mfa. R topics documented: July 11, 2018
Package mfa July 11, 2018 Title Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations Version 1.2.0 MFA models genomic bifurcations using a Bayesian hierarchical mixture
Package nima. May 23, 2018
Title Nima Hejazi's R Toolbox Version 0.5.0 Package nima May 23, 2018 Miscellaneous R functions developed over the course of statistical research and scientific computing. These include, for example, utilities
Package crossmeta. September 5, 2018
Package crossmeta September 5, 2018 Title Cross Platform Meta-Analysis of Microarray Data Version 1.6.0 Author Alex Pickering Maintainer Alex Pickering Implements cross-platform
Package desplot. R topics documented: April 3, 2018
Package desplot April 3, 2018 Title Plotting Field Plans for Agricultural Experiments Version 1.4 Date 2018-04-02 Type Package Description A function for plotting maps of agricultural field experiments
Package categorycompare
Version 1.24.0 Package categorycompare August 31, 2018 Title Meta-analysis of high-throughput experiments using feature annotations Author Robert M. Flight Maintainer Robert M. Flight