my-vignette
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
# library(clusterProfiler)
library(org.Sc.sgd.db)
#> Loading required package: AnnotationDbi
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#>
#> Attaching package: 'generics'
#> The following object is masked from 'package:dplyr':
#>
#> explain
#> The following objects are masked from 'package:base':
#>
#> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#> setequal, union
#>
#> Attaching package: 'BiocGenerics'
#> The following object is masked from 'package:dplyr':
#>
#> combine
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following object is masked from 'package:utils':
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#> data
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
#> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#> rbind, Reduce, rownames, sapply, saveRDS, scale, sequence, table,
#> tapply, transform, unique, unsplit, which.max, which.min
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: IRanges
#> Loading required package: S4Vectors
#>
#> Attaching package: 'S4Vectors'
#> The following objects are masked from 'package:dplyr':
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#> first, rename
#> The following object is masked from 'package:utils':
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#> findMatches
#> The following objects are masked from 'package:base':
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#> expand.grid, I, unname
#>
#> Attaching package: 'IRanges'
#> The following objects are masked from 'package:dplyr':
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#> collapse, desc, slice
#>
#> Attaching package: 'AnnotationDbi'
#> The following object is masked from 'package:dplyr':
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#> select
#> Tutorial for Paralogs
example_plot <- Paralogs::plotParalogs(
example_enrich_results,
lrt_yeast,
pathway_code = "sce04138",
# keytype = "ORF",
juke = 18,
title = "Example Title for this Plot"
)
#> Loading required namespace: DOSE
#>
#> adding rname 'https://rest.kegg.jp/get/map04138/image2x'
example_plot