oncogenetics / locusexplorer Goto Github PK

x = BP
y = Beta

Make simple manhattan plot when LD file is not supplied.

The format you're describing is actually bedGraph (http://genome.ucsc.edu/goldenpath/help/bedgraph.html) not BED (http://genome.ucsc.edu/FAQ/FAQformat.html#format1). The 4th field of BED is a name; the 4th field of bedGraph is a number.

When playing around with the region that should be displayed, one may receive error messages as:

chr2:172800000-NA
missing value where TRUE/FALSE needed

This should be fixed for better usability.

Instead of LNCAP display ENCODE bigwig tracks, as in UCSC browser.

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/

Might be dupilcate of #49

Again probably related to “Source” vs “source”. This time, “Source” seems to be required. After changing this in “server.R”, it works.

Theme choice for shades, classic, B&W?

Read bedGraph file, ignore track definition lines

http://genome.ucsc.edu/goldenpath/help/bedgraph.html

https://github.com/oncogenetics/LocusExplorer/blob/master/server.R#L98

Related issue: #40

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=209011996_katI9xnPw3NM0Pna2F5fP0iRjlbu&c=chr5&g=wgEncodeRegDnaseClustered

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegDnaseClustered/

Currently not hidden, development mode, on v1.0 onwards it will be hidden

Split Gene track to positive negative strand

LNCAP arrows for prostate data

Potential solution: start new clean R session, or #15, #37, and website version will cover this issue.

When trying the software in RStudio, we initially received the following error after running “runGitHub("LocusExplorer", "oncogenetics")” to start the tool:

Error in unloadNamespace(package) :
namespace ‘AnnotationDbi’ is imported by ‘geneplotter’, ‘VariantAnnotation’, ‘GenomicFeatures’, ‘annotate’, ‘genefilter’, ‘biomaRt’, ‘OrganismDbi’, ‘biovizBase’ so cannot be unloaded Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, :
Package ‘AnnotationDbi’ version 1.31.18 cannot be unloaded

It seems that if the session already imported particular packages, there can be a problem with LocusExplorer because AnnotationDbi cannot be unloaded due to dependencies.
It should be stated explicitly that an empty workspace should be used to start the tool to avoid this, or any other statement to tackle the problem.

App starts without prostate data. When Prostate data is selected, pop up to download prostate data from web.

Add suggestiveline and genomewideline to manhattan plot

https://github.com/oncogenetics/LocusExplorer/blob/master/Source/Manhattan.R

add tabix/plink tutorial

https://github.com/oncogenetics/LocusExplorer/blob/master/Markdown/LDTutorial.md

upload multiple bed tracks, display as one track.

Select gene tracks
UCSC
RefGene
GENCODE

1. "supplied BED file": "BED" --> "bedGraph", since the 4th column is numeric. - I think this issue is resolved. #40 ?

Replicate Figure 1 in manuscript

@EdSaunders Below are the points from the reviewer, I suggest we wait until we fix all other issues, then we can re-create the plot for Figure 1, so it will match with the latest version.

2.1 I tried to reproduce Figure 1 using Locus Explorer and noted a few differences. I suggest regenerating the image for Figure 1 using the latest version.

2.2. The LDSmooth curve shapes for rs718961 and rs11649743 are different -- in Figure 1 they have one peak and the pink curve is split at the top, while in Locus Explorer, they have a large peak plus a smaller peak to the right (depending on LD). I tried adjusting LD but none of the values (0, 0.05, 0.10, 0.15, and the default 0.20) seemed to duplicate the shapes in Figure 1.

2.3 I uploaded 3 images generated by LocusLink here: http://imgur.com/a/pgAGg (can be viewed only by those with the link) In the order that they're displayed, they show LD 0.15, 0.10 and 0.05. Compare the pink and olive-green curve shapes with Figure 1 (and the left & right ends of the SNPType and Histone tracks vs. Fig 1).

When I use the Example data in Plot Settings, and check all of the tracks, I can see data for all of them except for Histone - instead of data it has the message:

Please download Histone bigWig files!

And I don't see anything about how to incorporate those in the Help tabs.

https://github.com/oncogenetics/LocusExplorer/blob/master/Source/UDF.R#L31

Hi! I'm on Mac OS X 10.9.5; installed R 3.2.2, Cairo (1.14.2_1) and PostgreSQL (9.4.4) using homebrew; installed the required R packages as described in the "Required Software" section of README.md; and ran 'library(shiny)' and 'runGitHub("LocusExplorer", "oncogenetics")' as described.

Unfortunately when I visit the URL mentioned in the output (http://127.0.0.1:7074/) I get only the text:

ERROR: could not find function "windowsFonts"'

And I see the same error at the end of the output in R.

I'm not very familiar with R so I'm not sure how to proceed debugging this, but please let me know if there are diagnostic commands I could run or if you need more info.

Here is the R session from 'library shiny' onward:

> library(shiny)  
> runGitHub("LocusExplorer", "oncogenetics")
Downloading https://github.com/oncogenetics/LocusExplorer/archive/master.tar.gz

Listening on http://127.0.0.1:7074
data.table 1.9.6  For help type ?data.table or https://github.com/Rdatatable/data.table/wiki
The fastest way to learn (by data.table authors): https://www.datacamp.com/courses/data-analysis-the-data-table-way

Attaching package: ‘dplyr’

The following objects are masked from ‘package:data.table’:

    between, last

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:dplyr’:

    combine, intersect, setdiff, union

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist, unsplit

Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: ‘ggbio’

The following objects are masked from ‘package:ggplot2’:

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:dplyr’:

    rename

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:tidyr’:

    expand

The following objects are masked from ‘package:dplyr’:

    collapse, desc, slice

The following object is masked from ‘package:data.table’:

    shift

Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
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")'.


Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:dplyr’:

    select

Loading required package: DBI

Error in eval(expr, envir, enclos) : 
  could not find function "windowsFonts"
Error in eval(expr, envir, enclos) : 
  could not find function "windowsFonts"

Duplicate of #11

When i click on plotSettings directly after loading the app, I receive the following message: Error in nrow(plotDatGeneticMap()) :
error in evaluating the argument 'x' in selecting a method for function 'nrow': Error in nrow(plotDatGeneticMap()) :
incorrect length (0), expecting: 1309

Error in nrow(plotDatLD()) :
error in evaluating the argument 'x' in selecting a method for function 'nrow': Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column

Hi

I have been playing around with LocusExplorer on Mac OS X and in general it's working well but I've noticed that when I try to zoom into a smaller region such as chr2:173330000-173360000 in Plot Settings, instead of the manhattan plot I get this error:

Error : Aesthetics must either be length one, or the same length as the dataProblems:BP, BP, PLog

That also appears in the console output in R.

BTW I'm not seeing the Recombination track, if it is the only one checked, I see no tracks?

Thanks,
Angie

Related duplicate #35

With a clean session, I receive the following error: Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Warning in file(filename, "r", encoding = encoding) :cannot open file 'source/UDF.R': No such file or directory Error in file(filename, "r", encoding = encoding) : cannot open the connection

After downloading the zip file, I figured out why the error occurs: The “source” directory had a upper-case “S” and was therefore not recognized. After changing the directory to “source”, I got the LocusExplorer to work. This should also be fixed.

UCSC ENCODE track - 7 bigwig files

Not very user-friendly message because the user may not know where to download the file from, where to put it, etc. Should be more clear what to do in that case.
Update: I just saw that this message is listed in the FAQs. Maybe edit the error message and say (see FAQs for more details).

Related issue #39

The suggested filenames when saving a plot contains “ characters at the beginning and end The “ should be removed because not all file systems may handle this appropriately.

http://docs.docker.com/mac/started
http://dirk.eddelbuettel.com/papers/r_and_docker_sep2014.pdf
http://www.flaviobarros.net/2015/04/30/dockerizing-a-shiny-app/

Hover plot legend, with summary of input variables.

Currently no validation in place...

Currently, regions are fixed, would be good to add sliding window browsing option for prostate data.

To compare plots for the same region from different datasets.
Once the plot if finalised, press snapshot, jpeg will be saved in temp folder, which then displayed in Snapshot tab.

Currently defined as LNCAP file, change the naming.

Hyperlink or hover-over full title

MotifbreakR R/Bioconductor package may be a useful visualisation to incorporate into future updates.

https://github.com/Simon-Coetzee/motifBreakR
http://bioinformatics.oxfordjournals.org/content/early/2015/08/28/bioinformatics.btv470

Possible solution, needs testing.

http://stackoverflow.com/a/17332558/680068
https://cran.r-project.org/web/packages/FField/FField.pdf

p1 <- (ggplot(mtcars, aes(x = wt, y = mpg, label = rownames(mtcars))) + 
         geom_point() + geom_text() + ggtitle("Before"))
x.fact <- 100/max(mtcars$wt)
y.fact <- 100/max(mtcars$mpg)
coords <- FFieldPtRep(coords = cbind(mtcars$wt * x.fact, 
                                     mtcars$mpg * y.fact), rep.fact = 40)
x.t <- coords$x/x.fact
y.t <- coords$y/y.fact
p2 <- (ggplot(mtcars, aes(x = wt, y = mpg, label = rownames(mtcars))) + 
         geom_point() + geom_text(x = x.t, y = y.t) 
       #+ 
        # geom_segment(data = mtcars, xend = x.t, yend = y.t) + ggtitle("After")
       )
grid.arrange(p1, p2)

http://stackoverflow.com/questions/21004491/avoiding-overlapping-of-labels-with-direct-labels-and-ggplot2
http://directlabels.r-forge.r-project.org/

https://github.com/oncogenetics/LocusExplorer/blob/master/Source/Manhattan.R

Similar to prostate data, when multiple regions uploaded as one file, drop down menu to display multiple regions.