leekgroup / regionreport Goto Github PK
View Code? Open in Web Editor NEWGenerate HTML report for a set of genomic regions or DESeq2/edgeR results
Home Page: http://leekgroup.github.io/regionReport
Generate HTML report for a set of genomic regions or DESeq2/edgeR results
Home Page: http://leekgroup.github.io/regionReport
These are related to knitrBoostrap
1.0.0 issue jimhester/knitrBootstrap#40
Given Karthik's third point from http://f1000research.com/articles/4-105/v1, it sounds like a great idea for regionReport
to upload html files to a gh-pages
branch in GitHub if the directory is indeed a git repo and the repo exists in GitHub in a place where the user has access to.
This is somewhat similar to ropensci/git2r#18.
Just figuring out how to properly cite some dependencies for the derfinderReport
app note.
jimhester/knitrBootstrap#48
rstudio/rmarkdown#79
ramnathv/rCharts#408
I am using regionReport to create a report from my defined regions in the cattle genome (no annotation provided):
report <- renderReport(regions, "Example bumphunter", pvalueVars = NULL,
densityVars = c("Area" = "area", "Value" = "value", "Cluster Length" = "clusterL"
), significantVar = NULL, output = "report", outdir = "report", device = "png")
I got an error in the annotation part regarding sequence lengths. I checked my regions, and there are regions with 1 base, so I am assuming this can be the issue.
No annotationPackage supplied. Trying org.Hs.eg.db.
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
Quitting from lines 187-196 (DMR_report.Rmd)
Error in mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence", :
sequences chr8, chr2, chr3, chr18, chr19, chr11, chr10, chr17, chr14, chr4, chrX, chr9, chr21, chr1, chr13, chr5, chr6, chr16, chr7, chr12, chr15, chr20, chr22 have incompatible seqlengths:
- in 'x': 113319770, 136231102, 121005158, 65820629, 63449741, 106982474, 103308737, 73167244, 82403003, 120000601, 139009144, 105454467, 69862954, 158534110, 83472345, 120089316, 117806340, 81013979, 110682743, 87216183, 85007780, 71974595, 60773035
- in 'y': 146364022, 243199373, 198022430, 78077248, 59128983, 135006516, 135534747, 81195210, 107349540, 191154276, 155270560, 141213431, 48129895, 249250621, 115169878, 180915260, 171115067, 90354753, 159138663, 133851895, 102531392, 63025520, 51304566
#input file used
regions
GRanges object with 9013 ranges and 5 metadata columns:
seqnames ranges strand | value area cluster L clusterL
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric> <numeric> <integer>
[1] chr8 75774711 * | 2.949010 2.94901 15171 1 4
[2] chr2 51908666-51908808 * | 0.612535 2.45014 7016 27734 4
[3] chr3 45240960-45241205 * | -0.448404 3.58723 11459 29451 8
[4] chr18 18018893-18019002 * | 0.669870 1.33974 5206 15759 2
[5] chr3 52425936-52426038 * | -0.817302 1.63460 11511 6018 2
... ... ... ... . ... ... ... ... ...
[9009] chr22 50902400 * | -0.100129 0.100129 8774 1 1
[9010] chr24 22850168 * | -0.100121 0.100121 9363 1 8
[9011] chr4 27093075 * | -0.100118 0.100118 12293 1 2
[9012] chr11 41409299 * | -0.100041 0.100041 1774 1 3
[9013] chr2 73146781 * | -0.100036 0.100036 7167 1 3
-------
Thank you
example('renderReport', 'regionReport', ask=FALSE)
fails when using knitrBootstrap version 0.9.0. That's because knitrBootstrap::knit_bootstrap() returns NULL instead of the character vector with the name of the resulting HTML file. This problem is easily solvable, but first I need to make sure the bioc-git-svn bridge is working properly now that the repo lives in leekgroup. I also have to push the fix to the release branch.
Thanks to Peter Andrews for the bug report.
Hello,
First, thanks a lot for this wonderful package!
I am getting an error when generating an HTML report passing a ggplot2 theme to the DESeq2Report
function. The source code (regionReport/R/DESeq2Report.R
) shows that the error is due to the verification in line 175. Should the function ggplot2::is.theme()
be used instead of is()
in this line?
I'll appreciate you taking a look into this issue.
Best,
Hector
All the Bioconductor packages (including regionReport
) were installed via BiocManager::install()
using R (v4.3.1) installed via Homebrew.
library('pasilla')
#> Loading required package: DEXSeq
#> Loading required package: BiocParallel
#> Loading required package: Biobase
#> Loading required package: BiocGenerics
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> 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, intersect, is.unsorted, lapply, Map, mapply,
#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
#> table, tapply, union, unique, unsplit, which.max, which.min
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#>
#> Attaching package: 'matrixStats'
#> The following objects are masked from 'package:Biobase':
#>
#> anyMissing, rowMedians
#>
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#>
#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#> The following object is masked from 'package:Biobase':
#>
#> rowMedians
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: S4Vectors
#>
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#>
#> findMatches
#> The following objects are masked from 'package:base':
#>
#> expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: DESeq2
#> Loading required package: AnnotationDbi
#> Loading required package: RColorBrewer
library('DESeq2')
library('ggplot2')
library('regionReport')
data("pasillaDEXSeqDataSet")
countData <- counts(dxd)
colData <- colData(dxd)[, c('condition', 'type')]
# Create DESeqDataSet object from the pasilla package
dds <- DESeqDataSetFromMatrix(countData = countData,
colData = colData,
design = ~ condition)
# Perform the differential expression analysis
dds <- DESeq(dds)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> -- replacing outliers and refitting for 1 genes
#> -- DESeq argument 'minReplicatesForReplace' = 7
#> -- original counts are preserved in counts(dds)
#> estimating dispersions
#> fitting model and testing
dir.create('DESeq2-example', showWarnings = FALSE, recursive = TRUE)
# Create the HTML report
report <- DESeq2Report(dds, project = 'DESeq2 HTML report',
intgroup = c('condition', 'type'), outdir = 'DESeq2-example',
output = 'index', theme = theme_bw())
#> Error in is(theme, c("theme", "gg")): length(class2) == 1L is not TRUE
sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-apple-darwin22.4.0 (64-bit)
#> Running under: macOS Ventura 13.4.1
#>
#> Matrix products: default
#> BLAS: /usr/local/Cellar/openblas/0.3.23/lib/libopenblasp-r0.3.23.dylib
#> LAPACK: /usr/local/Cellar/r/4.3.1/lib/R/lib/libRlapack.dylib; LAPACK version 3.11.0
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> time zone: America/Chicago
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> loaded via a namespace (and not attached):
#> [1] digest_0.6.33 fastmap_1.1.1 xfun_0.39 glue_1.6.2
#> [5] knitr_1.43 htmltools_0.5.5 rmarkdown_2.23 lifecycle_1.0.3
#> [9] cli_3.6.1 reprex_2.0.2 withr_2.5.0 compiler_4.3.1
#> [13] rstudioapi_0.15.0 tools_4.3.1 evaluate_0.21 yaml_2.3.7
#> [17] rlang_1.1.1 fs_1.6.2
Hi,
When running regionReport
with the DESeq2Report
function, I get the below error:
Error in curl::curl_fetch_memory(url, handle = handle) :
Failed to connect to data.crossref.org port 80: No route to host
I think it's something related to the proxy or unavailability of the server.
Although the error seems to come from the dependency package curl
, is there a way to fix or bypass this in regionReport
?
How?
Basically, we need more than 1 observation per chr to make the density plots. See tidyverse/ggplot2#957
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