Basics

Install derfinderPlot

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. derfinderPlot is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can install derfinderPlot by using the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("derfinderPlot")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

Required knowledge

derfinderPlot is based on many other packages and in particular in those that have implemented the infrastructure needed for dealing with RNA-seq data. A derfinderPlot user is not expected to deal with those packages directly but will need to be familiar with derfinder and for some plots with ggbio.

If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.

Asking for help

As package developers, we try to explain clearly how to use our packages and in which order to use the functions. But R and Bioconductor have a steep learning curve so it is critical to learn where to ask for help. The blog post quoted above mentions some but we would like to highlight the Bioconductor support site as the main resource for getting help: remember to use the derfinder or derfinderPlot tags and check the older posts. Other alternatives are available such as creating GitHub issues and tweeting. However, please note that if you want to receive help you should adhere to the posting guidelines. It is particularly critical that you provide a small reproducible example and your session information so package developers can track down the source of the error.

Citing derfinderPlot

We hope that derfinderPlot will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("derfinderPlot")

## To cite package 'derfinderPlot' in publications use:
## 
##   Collado-Torres L, Jaffe AE, Leek JT (2017). _derfinderPlot: Plotting
##   functions for derfinder_. doi:10.18129/B9.bioc.derfinderPlot
##   <https://doi.org/10.18129/B9.bioc.derfinderPlot>,
##   https://github.com/leekgroup/derfinderPlot - R package version
##   1.41.0, <http://www.bioconductor.org/packages/derfinderPlot>.
## 
##   Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B,
##   Irizarry RA, Leek JT, Jaffe AE (2017). "Flexible expressed region
##   analysis for RNA-seq with derfinder." _Nucl. Acids Res._.
##   doi:10.1093/nar/gkw852 <https://doi.org/10.1093/nar/gkw852>,
##   <http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852>.
## 
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.

Introduction to derfinderPlot

derfinderPlot (Collado-Torres, Jaffe, and Leek, 2017) is an addon package for derfinder (Collado-Torres, Nellore, Frazee, Wilks, Love, Langmead, Irizarry, Leek, and Jaffe, 2017) with functions that allow you to visualize the results.

While the functions in derfinderPlot assume you generated the data with derfinder, they can be used with other GRanges objects properly formatted.

The functions in derfinderPlot are:

plotCluster() is a tailored ggbio (Yin, Cook, and Lawrence, 2012) plot that shows all the regions in a cluster (defined by distance). It shows the base-level coverage for each sample as well as the mean for each group. If these regions overlap any known gene, the gene and the transcript annotation is displayed.
plotOverview() is another tailored ggbio (Yin, Cook, and Lawrence, 2012) plot showing an overview of the whole genome. This plot can be useful to observe if the regions are clustered in a subset of a chromosome. It can also be used to check whether the regions match predominantly one part of the gene structure (for example, 3’ overlaps).
plotRegionCoverage() is a fast plotting function using R base graphics that shows the base-level coverage for each sample inside a specific region of the genome. If the region overlaps any known gene or intron, the information is displayed. Optionally, it can display the known transcripts. This function is most likely the easiest to use with GRanges objects from other packages.

Example

As an example, we will analyze a small subset of the samples from the BrainSpan Atlas of the Human Brain (BrainSpan, 2011) publicly available data.

We first load the required packages.

## Load libraries
suppressPackageStartupMessages(library("derfinder"))
library("derfinderData")
library("derfinderPlot")

## Registered S3 method overwritten by 'GGally':
##   method from   
##   +.gg   ggplot2

Analyze data

For this example, we created a small table with the relevant phenotype data for 12 samples: 6 from fetal samples and 6 from adult samples. We chose at random a brain region, in this case the primary auditory cortex (core) and for the example we will only look at data from chromosome 21. Other variables include the age in years and the gender. The data is shown below.

library("knitr")
## Get pheno table
pheno <- subset(brainspanPheno, structure_acronym == "A1C")

## Display the main information
p <- pheno[, -which(colnames(pheno) %in% c(
    "structure_acronym",
    "structure_name", "file"
))]
rownames(p) <- NULL
kable(p, format = "html", row.names = TRUE)

	gender	lab	Age	group
1	M	HSB114.A1C	-0.5192308	fetal
2	M	HSB103.A1C	-0.5192308	fetal
3	M	HSB178.A1C	-0.4615385	fetal
4	M	HSB154.A1C	-0.4615385	fetal
5	F	HSB150.A1C	-0.5384615	fetal
6	F	HSB149.A1C	-0.5192308	fetal
7	F	HSB130.A1C	21.0000000	adult
8	M	HSB136.A1C	23.0000000	adult
9	F	HSB126.A1C	30.0000000	adult
10	M	HSB145.A1C	36.0000000	adult
11	M	HSB123.A1C	37.0000000	adult
12	F	HSB135.A1C	40.0000000	adult

We can load the data from derfinderData (Collado-Torres, Jaffe, and Leek, 2024) by first identifying the paths to the BigWig files with derfinder::rawFiles() and then loading the data with derfinder::fullCoverage().

## Determine the files to use and fix the names
files <- rawFiles(system.file("extdata", "A1C", package = "derfinderData"),
    samplepatt = "bw", fileterm = NULL
)
names(files) <- gsub(".bw", "", names(files))

## Load the data from disk
system.time(fullCov <- fullCoverage(files = files, chrs = "chr21"))

## 2024-10-30 05:45:47.290979 fullCoverage: processing chromosome chr21

## 2024-10-30 05:45:47.302928 loadCoverage: finding chromosome lengths

## 2024-10-30 05:45:47.323242 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB103.bw

## 2024-10-30 05:45:47.46993 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB114.bw

## 2024-10-30 05:45:47.606987 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB123.bw

## 2024-10-30 05:45:47.702125 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB126.bw

## 2024-10-30 05:45:47.768818 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB130.bw

## 2024-10-30 05:45:47.858552 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB135.bw

## 2024-10-30 05:45:47.922148 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB136.bw

## 2024-10-30 05:45:47.989344 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB145.bw

## 2024-10-30 05:45:48.076263 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB149.bw

## 2024-10-30 05:45:48.156914 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB150.bw

## 2024-10-30 05:45:48.232102 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB154.bw

## 2024-10-30 05:45:48.329043 loadCoverage: loading BigWig file /github/workspace/pkglib/derfinderData/extdata/A1C/HSB178.bw

## 2024-10-30 05:45:49.223264 loadCoverage: applying the cutoff to the merged data

## 2024-10-30 05:45:49.243991 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered.

##    user  system elapsed 
##   1.970   0.028   1.998

Alternatively, since the BigWig files are publicly available from BrainSpan (see here), we can extract the relevant coverage data using derfinder::fullCoverage(). Note that as of rtracklayer 1.25.16 BigWig files are not supported on Windows: you can find the fullCov object inside derfinderData to follow the examples.

## Determine the files to use and fix the names
files <- pheno$file
names(files) <- gsub(".A1C", "", pheno$lab)

## Load the data from the web
system.time(fullCov <- fullCoverage(files = files, chrs = "chr21"))

Once we have the base-level coverage data for all 12 samples, we can construct the models. In this case, we want to find differences between fetal and adult samples while adjusting for gender and a proxy of the library size.

## Get some idea of the library sizes
sampleDepths <- sampleDepth(collapseFullCoverage(fullCov), 1)

## 2024-10-30 05:45:49.321298 sampleDepth: Calculating sample quantiles

## 2024-10-30 05:45:49.401524 sampleDepth: Calculating sample adjustments

## Define models
models <- makeModels(sampleDepths,
    testvars = pheno$group,
    adjustvars = pheno[, c("gender")]
)

Next, we can find candidate differentially expressed regions (DERs) using as input the segments of the genome where at least one sample has coverage greater than 3. In this particular example, we chose a low theoretical F-statistic cutoff and used 20 permutations.

## Filter coverage
filteredCov <- lapply(fullCov, filterData, cutoff = 3)

## 2024-10-30 05:45:49.641668 filterData: originally there were 48129895 rows, now there are 90023 rows. Meaning that 99.81 percent was filtered.

## Perform differential expression analysis
suppressPackageStartupMessages(library("bumphunter"))
system.time(results <- analyzeChr(
    chr = "chr21", filteredCov$chr21,
    models, groupInfo = pheno$group, writeOutput = FALSE,
    cutoffFstat = 5e-02, nPermute = 20, seeds = 20140923 + seq_len(20)
))

## 2024-10-30 05:45:50.571039 analyzeChr: Pre-processing the coverage data

## 2024-10-30 05:45:51.866829 analyzeChr: Calculating statistics

## 2024-10-30 05:45:51.869407 calculateStats: calculating the F-statistics

## 2024-10-30 05:45:51.998141 analyzeChr: Calculating pvalues

## 2024-10-30 05:45:51.998847 analyzeChr: Using the following theoretical cutoff for the F-statistics 5.31765507157871

## 2024-10-30 05:45:52.000106 calculatePvalues: identifying data segments

## 2024-10-30 05:45:52.007249 findRegions: segmenting information

## 2024-10-30 05:45:52.038273 findRegions: identifying candidate regions

## 2024-10-30 05:45:52.089237 findRegions: identifying region clusters

## 2024-10-30 05:45:52.186609 calculatePvalues: calculating F-statistics for permutation 1 and seed 20140924

## 2024-10-30 05:45:52.299255 findRegions: segmenting information

## 2024-10-30 05:45:52.326331 findRegions: identifying candidate regions

## 2024-10-30 05:45:52.384212 calculatePvalues: calculating F-statistics for permutation 2 and seed 20140925

## 2024-10-30 05:45:52.502136 findRegions: segmenting information

## 2024-10-30 05:45:52.528964 findRegions: identifying candidate regions

## 2024-10-30 05:45:52.570482 calculatePvalues: calculating F-statistics for permutation 3 and seed 20140926

## 2024-10-30 05:45:52.697095 findRegions: segmenting information

## 2024-10-30 05:45:52.724653 findRegions: identifying candidate regions

## 2024-10-30 05:45:52.76721 calculatePvalues: calculating F-statistics for permutation 4 and seed 20140927

## 2024-10-30 05:45:52.891298 findRegions: segmenting information

## 2024-10-30 05:45:52.918767 findRegions: identifying candidate regions

## 2024-10-30 05:45:52.961642 calculatePvalues: calculating F-statistics for permutation 5 and seed 20140928

## 2024-10-30 05:45:53.082798 findRegions: segmenting information

## 2024-10-30 05:45:53.109737 findRegions: identifying candidate regions

## 2024-10-30 05:45:53.151353 calculatePvalues: calculating F-statistics for permutation 6 and seed 20140929

## 2024-10-30 05:45:53.278686 findRegions: segmenting information

## 2024-10-30 05:45:53.305925 findRegions: identifying candidate regions

## 2024-10-30 05:45:53.348425 calculatePvalues: calculating F-statistics for permutation 7 and seed 20140930

## 2024-10-30 05:45:53.472527 findRegions: segmenting information

## 2024-10-30 05:45:53.499543 findRegions: identifying candidate regions

## 2024-10-30 05:45:53.541557 calculatePvalues: calculating F-statistics for permutation 8 and seed 20140931

## 2024-10-30 05:45:53.670149 findRegions: segmenting information

## 2024-10-30 05:45:53.697205 findRegions: identifying candidate regions

## 2024-10-30 05:45:53.739056 calculatePvalues: calculating F-statistics for permutation 9 and seed 20140932

## 2024-10-30 05:45:53.866207 findRegions: segmenting information

## 2024-10-30 05:45:53.894046 findRegions: identifying candidate regions

## 2024-10-30 05:45:53.937964 calculatePvalues: calculating F-statistics for permutation 10 and seed 20140933

## 2024-10-30 05:45:54.061508 findRegions: segmenting information

## 2024-10-30 05:45:54.088749 findRegions: identifying candidate regions

## 2024-10-30 05:45:54.130578 calculatePvalues: calculating F-statistics for permutation 11 and seed 20140934

## 2024-10-30 05:45:54.252267 findRegions: segmenting information

## 2024-10-30 05:45:54.279226 findRegions: identifying candidate regions

## 2024-10-30 05:45:54.321364 calculatePvalues: calculating F-statistics for permutation 12 and seed 20140935

## 2024-10-30 05:45:54.448265 findRegions: segmenting information

## 2024-10-30 05:45:54.475616 findRegions: identifying candidate regions

## 2024-10-30 05:45:54.519212 calculatePvalues: calculating F-statistics for permutation 13 and seed 20140936

## 2024-10-30 05:45:54.64929 findRegions: segmenting information

## 2024-10-30 05:45:54.676754 findRegions: identifying candidate regions

## 2024-10-30 05:45:54.719918 calculatePvalues: calculating F-statistics for permutation 14 and seed 20140937

## 2024-10-30 05:45:55.647879 findRegions: segmenting information

## 2024-10-30 05:45:55.674853 findRegions: identifying candidate regions

## 2024-10-30 05:45:55.71657 calculatePvalues: calculating F-statistics for permutation 15 and seed 20140938

## 2024-10-30 05:45:55.837188 findRegions: segmenting information

## 2024-10-30 05:45:55.866058 findRegions: identifying candidate regions

## 2024-10-30 05:45:55.907748 calculatePvalues: calculating F-statistics for permutation 16 and seed 20140939

## 2024-10-30 05:45:56.029791 findRegions: segmenting information

## 2024-10-30 05:45:56.057525 findRegions: identifying candidate regions

## 2024-10-30 05:45:56.098849 calculatePvalues: calculating F-statistics for permutation 17 and seed 20140940

## 2024-10-30 05:45:56.21142 findRegions: segmenting information

## 2024-10-30 05:45:56.2381 findRegions: identifying candidate regions

## 2024-10-30 05:45:56.278898 calculatePvalues: calculating F-statistics for permutation 18 and seed 20140941

## 2024-10-30 05:45:56.39836 findRegions: segmenting information

## 2024-10-30 05:45:56.42607 findRegions: identifying candidate regions

## 2024-10-30 05:45:56.467728 calculatePvalues: calculating F-statistics for permutation 19 and seed 20140942

## 2024-10-30 05:45:56.591923 findRegions: segmenting information

## 2024-10-30 05:45:56.61913 findRegions: identifying candidate regions

## 2024-10-30 05:45:56.661023 calculatePvalues: calculating F-statistics for permutation 20 and seed 20140943

## 2024-10-30 05:45:56.77408 findRegions: segmenting information

## 2024-10-30 05:45:56.80163 findRegions: identifying candidate regions

## 2024-10-30 05:45:56.865969 calculatePvalues: calculating the p-values

## 2024-10-30 05:45:56.912657 analyzeChr: Annotating regions

## No annotationPackage supplied. Trying org.Hs.eg.db.

## Loading required package: org.Hs.eg.db

## Loading required package: AnnotationDbi

## 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")'.

##

## Getting TSS and TSE.

## Getting CSS and CSE.

## Getting exons.

## Annotating genes.

## ...

##    user  system elapsed 
##  42.932   7.161  42.032

## Quick access to the results
regions <- results$regions$regions

## Annotation database to use
suppressPackageStartupMessages(library("TxDb.Hsapiens.UCSC.hg19.knownGene"))
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

`plotOverview()`

Now that we have obtained the main results using derfinder, we can proceed to visualizing the results using derfinderPlot. The easiest to use of all the functions is plotOverview() which takes a set of regions and annotation information produced by bumphunter::matchGenes().

Figure @ref(fig:plotOverview) shows the candidate DERs colored by whether their q-value was less than 0.10 or not.

## Q-values overview
plotOverview(regions = regions, annotation = results$annotation, type = "qval")

## 2024-10-30 05:46:32.721407 plotOverview: assigning chromosome lengths from hg19!

## Scale for x is already present.
## Adding another scale for x, which will replace the existing scale.
## Scale for x is already present.
## Adding another scale for x, which will replace the existing scale.

Location of the DERs in the genome. This plot is was designed for many chromosomes but only one is shown here for simplicity.

Figure @ref(fig:plotOverview2) shows the candidate DERs colored by the type of gene feature they are nearest too.

## Annotation overview
plotOverview(
    regions = regions, annotation = results$annotation,
    type = "annotation"
)

## 2024-10-30 05:46:34.133483 plotOverview: assigning chromosome lengths from hg19!

## Scale for x is already present.
## Adding another scale for x, which will replace the existing scale.

Location of the DERs in the genome and colored by annotation class. This plot is was designed for many chromosomes but only one is shown here for simplicity.

In this particular example, because we are only using data from one chromosome the above plot is not as informative as in a real case scenario. However, with this plot we can quickly observe that nearly all of the candidate DERs are inside an exon.

`plotRegionCoverage()`

The complete opposite of visualizing the candidate DERs at the genome-level is to visualize them one region at a time. plotRegionCoverage() allows us to do this quickly for a large number of regions.

Before using this function, we need to process more detailed information using two derfinder functions: annotateRegions() and getRegionCoverage() as shown below.

## Get required information for the plots
annoRegs <- annotateRegions(regions, genomicState$fullGenome)

## 2024-10-30 05:46:34.763665 annotateRegions: counting

## 2024-10-30 05:46:34.816212 annotateRegions: annotating

regionCov <- getRegionCoverage(fullCov, regions)

## 2024-10-30 05:46:34.895705 getRegionCoverage: processing chr21

## 2024-10-30 05:46:34.935381 getRegionCoverage: done processing chr21

Once we have the relevant information we can proceed to plotting the first 10 regions. In this case, we will supply plotRegionCoverage() with the information it needs to plot transcripts overlapping these 10 regions (Figures @ref(fig:plotRegCov1), @ref(fig:plotRegCov2), @ref(fig:plotRegCov3), @ref(fig:plotRegCov4), @ref(fig:plotRegCov5), @ref(fig:plotRegCov6), @ref(fig:plotRegCov7), @ref(fig:plotRegCov8), @ref(fig:plotRegCov9), @ref(fig:plotRegCov10)).

## Plot top 10 regions
plotRegionCoverage(
    regions = regions, regionCoverage = regionCov,
    groupInfo = pheno$group, nearestAnnotation = results$annotation,
    annotatedRegions = annoRegs, whichRegions = 1:10, txdb = txdb, scalefac = 1,
    ask = FALSE, verbose = FALSE
)

Base-pair resolution plot of differentially expressed region 1.

Base-pair resolution plot of differentially expressed region 2.

Base-pair resolution plot of differentially expressed region 3.

Base-pair resolution plot of differentially expressed region 4.

Base-pair resolution plot of differentially expressed region 5.

Base-pair resolution plot of differentially expressed region 6.

Base-pair resolution plot of differentially expressed region 7.

Base-pair resolution plot of differentially expressed region 8.

Base-pair resolution plot of differentially expressed region 9.

Base-pair resolution plot of differentially expressed region 10.

The base-level coverage is shown in a log2 scale with any overlapping exons shown in dark blue and known introns in light blue.

`plotCluster()`

In this example, we noticed with the plotRegionCoverage() plots that most of the candidate DERs are contained in known exons. Sometimes, the signal might be low or we might have used very stringent cutoffs in the derfinder analysis. One way we can observe this is by plotting clusters of regions where a cluster is defined as regions within 300 bp (default option) of each other.

To visualize the clusters, we can use plotCluster() which takes similar input to plotOverview() with the notable addition of the coverage information as well as the idx argument. This argument specifies which region to focus on: it will be plotted with a red bar and will determine the cluster to display.

In Figure @ref(fig:plotCluster) we observe one large candidate DER with other nearby ones that do not have a q-value less than 0.10. In a real analysis, we would probably discard this region as the coverage is fairly low.

## First cluster
plotCluster(
    idx = 1, regions = regions, annotation = results$annotation,
    coverageInfo = fullCov$chr21, txdb = txdb, groupInfo = pheno$group,
    titleUse = "pval"
)

## Parsing transcripts...

## Parsing exons...

## Parsing cds...

## Parsing utrs...

## ------exons...

## ------cdss...

## ------introns...

## ------utr...

## aggregating...

## Done

## Constructing graphics...

Cluster plot for cluster 1 using ggbio.

The second cluster (Figure @ref(fig:plotCluster2)) shows a larger number of potential DERs (again without q-values less than 0.10) in a segment of the genome where the coverage data is highly variable. This is a common occurrence with RNA-seq data.

## Second cluster
plotCluster(
    idx = 2, regions = regions, annotation = results$annotation,
    coverageInfo = fullCov$chr21, txdb = txdb, groupInfo = pheno$group,
    titleUse = "pval"
)

## Parsing transcripts...

## Parsing exons...

## Parsing cds...

## Parsing utrs...

## ------exons...

## ------cdss...

## ------introns...

## ------utr...

## aggregating...

## Done

## Constructing graphics...

## Warning in !vapply(ggl, fixed, logical(1L)) & !vapply(PlotList, is, "Ideogram",
## : longer object length is not a multiple of shorter object length

## Warning in scale_y_continuous(trans = log2_trans()): log-2 transformation
## introduced infinite values.

Cluster plot for cluster 2 using ggbio.

These plots show an ideogram which helps quickly identify which region of the genome we are focusing on. Then, the base-level coverage information for each sample is displayed in log2. Next, the coverage group means are shown in the log2 scale. The plot is completed with the potential and candidate DERs as well as any known transcripts.

`vennRegions`

derfinder has functions for annotating regions given their genomic state. A typical visualization is to then view how many regions overlap known exons, introns, intergenic regions, none of them or several of these groups in a venn diagram. The function vennRegions() makes this plot using the output from derfinder::annotateRegions() as shown in Figure @ref(fig:vennRegions).

## Make venn diagram
venn <- vennRegions(annoRegs)

Venn diagram of regions by annotation class.

## It returns the actual venn counts information
venn

##   exon intergenic intron Counts
## 1    0          0      0      0
## 2    0          0      1      2
## 3    0          1      0      4
## 4    0          1      1      0
## 5    1          0      0    259
## 6    1          0      1     35
## 7    1          1      0      0
## 8    1          1      1      0
## attr(,"class")
## [1] "VennCounts"

Reproducibility

This package was made possible thanks to:

R (R Core Team, 2024)
GenomeInfoDb (Arora, Morgan, Carlson, and Pagès, 2017)
GenomicRanges (Lawrence, Huber, Pagès, Aboyoun, Carlson, Gentleman, Morgan, and Carey, 2013)
ggbio (Yin, Cook, and Lawrence, 2012)
ggplot2 (Wickham, 2016)
IRanges (Lawrence, Huber, Pagès et al., 2013)
plyr (Wickham, 2011)
RColorBrewer (Neuwirth, 2022)
reshape2 (Wickham, 2007)
scales (Wickham, Pedersen, and Seidel, 2023)
biovizBase (Yin, Lawrence, and Cook, 2024)
bumphunter (Jaffe, Murakami, Lee, Leek, Fallin, Feinberg, and Irizarry, 2012) and (Jaffe, Murakami, Lee, Leek, Fallin, Feinberg, and Irizarry, 2012)
derfinder (Collado-Torres, Nellore, Frazee et al., 2017)
derfinderData (Collado-Torres, Jaffe, and Leek, 2024)
sessioninfo (Wickham, Chang, Flight, Müller, and Hester, 2021)
knitr (Xie, 2014)
BiocStyle (Oleś, 2024)
RefManageR (McLean, 2017)
rmarkdown (Allaire, Xie, Dervieux, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2024)
testthat (Wickham, 2011)
TxDb.Hsapiens.UCSC.hg19.knownGene (Carlson and Maintainer, 2015)

Code for creating the vignette

## Create the vignette
library("rmarkdown")
system.time(render("derfinderPlot.Rmd", "BiocStyle::html_document"))

## Extract the R code
library("knitr")
knit("derfinderPlot.Rmd", tangle = TRUE)

## Clean up
unlink("chr21", recursive = TRUE)

Date the vignette was generated.

## [1] "2024-10-30 05:46:49 UTC"

Wallclock time spent generating the vignette.

## Time difference of 1.247 mins

R session information.

## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.4.1 (2024-06-14)
##  os       Ubuntu 24.04.1 LTS
##  system   x86_64, linux-gnu
##  ui       X11
##  language (EN)
##  collate  C
##  ctype    en_US.UTF-8
##  tz       Etc/UTC
##  date     2024-10-30
##  pandoc   3.2.1 @ /usr/local/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package                           * version   date (UTC) lib source
##  abind                               1.4-8     2024-09-12 [2] RSPM (R 4.4.0)
##  AnnotationDbi                     * 1.69.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  AnnotationFilter                    1.31.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  backports                           1.5.0     2024-05-23 [2] RSPM (R 4.4.0)
##  base64enc                           0.1-3     2015-07-28 [2] RSPM (R 4.4.0)
##  bibtex                              0.5.1     2023-01-26 [2] RSPM (R 4.4.0)
##  Biobase                           * 2.67.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  BiocFileCache                       2.15.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  BiocGenerics                      * 0.53.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  BiocIO                              1.17.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  BiocManager                         1.30.25   2024-08-28 [2] RSPM (R 4.4.0)
##  BiocParallel                        1.39.0    2024-10-23 [2] https://bioc.r-universe.dev (R 4.4.1)
##  BiocStyle                         * 2.35.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  biomaRt                             2.63.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  Biostrings                          2.75.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  biovizBase                          1.55.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  bit                                 4.5.0     2024-09-20 [2] RSPM (R 4.4.0)
##  bit64                               4.5.2     2024-09-22 [2] RSPM (R 4.4.0)
##  bitops                              1.0-9     2024-10-03 [2] RSPM (R 4.4.0)
##  blob                                1.2.4     2023-03-17 [2] RSPM (R 4.4.0)
##  BSgenome                            1.73.1    2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  bslib                               0.8.0     2024-07-29 [2] RSPM (R 4.4.0)
##  buildtools                          1.0.0     2024-10-28 [3] local (/pkg)
##  bumphunter                        * 1.49.0    2024-10-30 [2] https://bioc.r-universe.dev (R 4.4.1)
##  cachem                              1.1.0     2024-05-16 [2] RSPM (R 4.4.0)
##  checkmate                           2.3.2     2024-07-29 [2] RSPM (R 4.4.0)
##  cli                                 3.6.3     2024-06-21 [2] RSPM (R 4.4.0)
##  cluster                             2.1.6     2023-12-01 [2] RSPM (R 4.4.0)
##  codetools                           0.2-20    2024-03-31 [2] RSPM (R 4.4.0)
##  colorspace                          2.1-1     2024-07-26 [2] RSPM (R 4.4.0)
##  crayon                              1.5.3     2024-06-20 [2] RSPM (R 4.4.0)
##  curl                                5.2.3     2024-09-20 [2] RSPM (R 4.4.0)
##  data.table                          1.16.2    2024-10-10 [2] RSPM (R 4.4.0)
##  DBI                                 1.2.3     2024-06-02 [2] RSPM (R 4.4.0)
##  dbplyr                              2.5.0     2024-03-19 [2] RSPM (R 4.4.0)
##  DelayedArray                        0.31.14   2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  derfinder                         * 1.39.0    2024-10-16 [2] https://bioc.r-universe.dev (R 4.4.1)
##  derfinderData                     * 2.23.0    2024-05-02 [2] Bioconductor 3.20 (R 4.4.1)
##  derfinderHelper                     1.39.0    2024-10-17 [2] https://bioc.r-universe.dev (R 4.4.1)
##  derfinderPlot                     * 1.41.0    2024-10-30 [1] https://bioc.r-universe.dev (R 4.4.1)
##  dichromat                           2.0-0.1   2022-05-02 [2] RSPM (R 4.4.0)
##  digest                              0.6.37    2024-08-19 [2] RSPM (R 4.4.0)
##  doRNG                               1.8.6     2023-01-16 [2] RSPM (R 4.4.0)
##  dplyr                               1.1.4     2023-11-17 [2] RSPM (R 4.4.0)
##  ensembldb                           2.29.1    2024-10-21 [2] https://bioc.r-universe.dev (R 4.4.1)
##  evaluate                            1.0.1     2024-10-10 [2] RSPM (R 4.4.0)
##  fansi                               1.0.6     2023-12-08 [2] RSPM (R 4.4.0)
##  farver                              2.1.2     2024-05-13 [2] RSPM (R 4.4.0)
##  fastmap                             1.2.0     2024-05-15 [2] RSPM (R 4.4.0)
##  filelock                            1.0.3     2023-12-11 [2] RSPM (R 4.4.0)
##  foreach                           * 1.5.2     2022-02-02 [2] RSPM (R 4.4.0)
##  foreign                             0.8-87    2024-06-26 [2] RSPM (R 4.4.0)
##  Formula                             1.2-5     2023-02-24 [2] RSPM (R 4.4.0)
##  generics                            0.1.3     2022-07-05 [2] RSPM (R 4.4.0)
##  GenomeInfoDb                      * 1.41.2    2024-10-02 [2] https://bioc.r-universe.dev (R 4.4.1)
##  GenomeInfoDbData                    1.2.13    2024-10-30 [2] Bioconductor
##  GenomicAlignments                   1.41.0    2024-10-28 [2] https://bioc.r-universe.dev (R 4.4.1)
##  GenomicFeatures                   * 1.57.1    2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  GenomicFiles                        1.41.0    2024-10-28 [2] https://bioc.r-universe.dev (R 4.4.1)
##  GenomicRanges                     * 1.57.2    2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  GGally                              2.2.1     2024-02-14 [2] RSPM (R 4.4.0)
##  ggbio                               1.53.0    2024-10-28 [2] https://bioc.r-universe.dev (R 4.4.1)
##  ggplot2                             3.5.1     2024-04-23 [2] RSPM (R 4.4.0)
##  ggstats                             0.7.0     2024-09-22 [2] RSPM (R 4.4.0)
##  glue                                1.8.0     2024-09-30 [2] RSPM (R 4.4.0)
##  graph                               1.83.0    2024-10-01 [2] https://bioc.r-universe.dev (R 4.4.1)
##  gridExtra                           2.3       2017-09-09 [2] RSPM (R 4.4.0)
##  gtable                              0.3.6     2024-10-25 [2] RSPM (R 4.4.0)
##  highr                               0.11      2024-05-26 [2] RSPM (R 4.4.0)
##  Hmisc                               5.2-0     2024-10-28 [2] RSPM (R 4.4.0)
##  hms                                 1.1.3     2023-03-21 [2] RSPM (R 4.4.0)
##  htmlTable                           2.4.3     2024-07-21 [2] RSPM (R 4.4.0)
##  htmltools                           0.5.8.1   2024-04-04 [2] RSPM (R 4.4.0)
##  htmlwidgets                         1.6.4     2023-12-06 [2] RSPM (R 4.4.0)
##  httr                                1.4.7     2023-08-15 [2] RSPM (R 4.4.0)
##  httr2                               1.0.5     2024-09-26 [2] RSPM (R 4.4.0)
##  IRanges                           * 2.39.2    2024-10-25 [2] https://bioc.r-universe.dev (R 4.4.1)
##  iterators                         * 1.0.14    2022-02-05 [2] RSPM (R 4.4.0)
##  jquerylib                           0.1.4     2021-04-26 [2] RSPM (R 4.4.0)
##  jsonlite                            1.8.9     2024-09-20 [2] RSPM (R 4.4.0)
##  KEGGREST                            1.45.1    2024-10-16 [2] https://bioc.r-universe.dev (R 4.4.1)
##  knitr                             * 1.48      2024-07-07 [2] RSPM (R 4.4.0)
##  labeling                            0.4.3     2023-08-29 [2] RSPM (R 4.4.0)
##  lattice                             0.22-6    2024-03-20 [2] RSPM (R 4.4.0)
##  lazyeval                            0.2.2     2019-03-15 [2] RSPM (R 4.4.0)
##  lifecycle                           1.0.4     2023-11-07 [2] RSPM (R 4.4.0)
##  limma                               3.61.12   2024-10-01 [2] https://bioc.r-universe.dev (R 4.4.1)
##  locfit                            * 1.5-9.10  2024-06-24 [2] RSPM (R 4.4.0)
##  lubridate                           1.9.3     2023-09-27 [2] RSPM (R 4.4.0)
##  magrittr                            2.0.3     2022-03-30 [2] RSPM (R 4.4.0)
##  maketools                           1.3.1     2024-10-28 [3] Github (jeroen/maketools@d46f92c)
##  Matrix                              1.7-1     2024-10-18 [2] RSPM (R 4.4.0)
##  MatrixGenerics                      1.17.1    2024-10-23 [2] https://bioc.r-universe.dev (R 4.4.1)
##  matrixStats                         1.4.1     2024-09-08 [2] RSPM (R 4.4.0)
##  memoise                             2.0.1     2021-11-26 [2] RSPM (R 4.4.0)
##  munsell                             0.5.1     2024-04-01 [2] RSPM (R 4.4.0)
##  nnet                                7.3-19    2023-05-03 [2] RSPM (R 4.4.0)
##  org.Hs.eg.db                      * 3.20.0    2024-10-30 [2] Bioconductor
##  OrganismDbi                         1.47.0    2024-10-11 [2] https://bioc.r-universe.dev (R 4.4.1)
##  pillar                              1.9.0     2023-03-22 [2] RSPM (R 4.4.0)
##  pkgconfig                           2.0.3     2019-09-22 [2] RSPM (R 4.4.0)
##  plyr                                1.8.9     2023-10-02 [2] RSPM (R 4.4.0)
##  png                                 0.1-8     2022-11-29 [2] RSPM (R 4.4.0)
##  prettyunits                         1.2.0     2023-09-24 [2] RSPM (R 4.4.0)
##  progress                            1.2.3     2023-12-06 [2] RSPM (R 4.4.0)
##  ProtGenerics                        1.37.1    2024-10-22 [2] https://bioc.r-universe.dev (R 4.4.1)
##  purrr                               1.0.2     2023-08-10 [2] RSPM (R 4.4.0)
##  qvalue                              2.37.0    2024-10-01 [2] https://bioc.r-universe.dev (R 4.4.1)
##  R6                                  2.5.1     2021-08-19 [2] RSPM (R 4.4.0)
##  rappdirs                            0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
##  RBGL                                1.81.0    2024-10-18 [2] https://bioc.r-universe.dev (R 4.4.1)
##  RColorBrewer                        1.1-3     2022-04-03 [2] RSPM (R 4.4.0)
##  Rcpp                                1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
##  RCurl                               1.98-1.16 2024-07-11 [2] RSPM (R 4.4.0)
##  RefManageR                        * 1.4.0     2022-09-30 [2] RSPM (R 4.4.0)
##  reshape2                            1.4.4     2020-04-09 [2] RSPM (R 4.4.0)
##  restfulr                            0.0.15    2022-06-16 [2] RSPM (R 4.4.1)
##  rjson                               0.2.23    2024-09-16 [2] RSPM (R 4.4.0)
##  rlang                               1.1.4     2024-06-04 [2] RSPM (R 4.4.0)
##  rmarkdown                           2.28      2024-08-17 [2] RSPM (R 4.4.0)
##  rngtools                            1.5.2     2021-09-20 [2] RSPM (R 4.4.0)
##  rpart                               4.1.23    2023-12-05 [2] RSPM (R 4.4.0)
##  Rsamtools                           2.21.2    2024-10-26 [2] https://bioc.r-universe.dev (R 4.4.1)
##  RSQLite                             2.3.7     2024-05-27 [2] RSPM (R 4.4.0)
##  rstudioapi                          0.17.1    2024-10-22 [2] RSPM (R 4.4.0)
##  rtracklayer                         1.65.0    2024-10-23 [2] https://bioc.r-universe.dev (R 4.4.1)
##  S4Arrays                            1.5.11    2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  S4Vectors                         * 0.43.2    2024-10-17 [2] https://bioc.r-universe.dev (R 4.4.1)
##  sass                                0.4.9     2024-03-15 [2] RSPM (R 4.4.0)
##  scales                              1.3.0     2023-11-28 [2] RSPM (R 4.4.0)
##  sessioninfo                       * 1.2.2     2021-12-06 [2] RSPM (R 4.4.0)
##  SparseArray                         1.5.45    2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  statmod                             1.5.0     2023-01-06 [2] RSPM (R 4.4.0)
##  stringi                             1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
##  stringr                             1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
##  SummarizedExperiment                1.35.5    2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  sys                                 3.4.3     2024-10-04 [2] RSPM (R 4.4.0)
##  tibble                              3.2.1     2023-03-20 [2] RSPM (R 4.4.0)
##  tidyr                               1.3.1     2024-01-24 [2] RSPM (R 4.4.0)
##  tidyselect                          1.2.1     2024-03-11 [2] RSPM (R 4.4.0)
##  timechange                          0.3.0     2024-01-18 [2] RSPM (R 4.4.0)
##  TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2     2024-10-30 [2] Bioconductor
##  txdbmaker                           1.1.2     2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  UCSC.utils                          1.1.0     2024-10-29 [2] https://bioc.r-universe.dev (R 4.4.1)
##  utf8                                1.2.4     2023-10-22 [2] RSPM (R 4.4.0)
##  VariantAnnotation                   1.51.2    2024-10-24 [2] https://bioc.r-universe.dev (R 4.4.1)
##  vctrs                               0.6.5     2023-12-01 [2] RSPM (R 4.4.0)
##  withr                               3.0.2     2024-10-28 [2] RSPM (R 4.4.0)
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##  XVector                             0.45.0    2024-10-02 [2] https://bioc.r-universe.dev (R 4.4.1)
##  yaml                                2.3.10    2024-07-26 [2] RSPM (R 4.4.0)
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## 
##  [1] /tmp/RtmpzCrfqY/Rinst22ec68edb3bc
##  [2] /github/workspace/pkglib
##  [3] /usr/local/lib/R/site-library
##  [4] /usr/lib/R/site-library
##  [5] /usr/lib/R/library
## 
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

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This vignette was generated using BiocStyle (Oleś, 2024) with knitr (Xie, 2014) and rmarkdown (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.

Citations made with RefManageR (McLean, 2017).

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[23] T. Yin, M. Lawrence, and D. Cook. biovizBase: Basic graphic utilities for visualization of genomic data. R package version 1.55.0. 2024.