przemol / seqplots Goto Github PK

I keep getting "Unknown genome name/genome not installed! Use UCSC compatible or contact administrator" error when uploading files. I did install the genome (HG19) in R.

While uploading the BED and BedGraph file , it is showing me the following error. I chose 'custom' as the genome, as there was no human genome in the drop down list.
What should I do?

seqplots failed to launch. received following error:

PROGRESS:15
Loading required package: DBI
Loading required package: methods
Error in sqliteSendQuery(con, statement, bind.data) :
error in statement: no such table: files
In addition: Warning message:
In strptime(x, fmt, tz = "GMT") :
unknown timezone 'zone/tz/2018c.1.0/zoneinfo/America/Los_Angeles'

I tried to load the self-forged genome to the SeqPlots by "install from file". But it didn't show up on the installed genome even I copied whole forged genome folder to the genome folder under SeqPlots. I would appreciate you can give a bit more details on how to install a forged genome from local file. Thanks.

Dear Author,
What is the best way? I dont want to create a binned file (I want the maximum resolution). Which tool do you usually use for converting bam files to one of the required in seqplots?
Thanks

Hi：
I am wondering how to use supersom? Two parameters (Grid-X and Grid-Y) can be adjusted? What does it mean?

For example, the above figure show the result from hclust. But I am more interesting in those regions with more on the center area, while less values in left and right area. Can I use supersom to better cluster the matrix?
Thanks.

Hi
After select the tracks and features I tried to "run the calculation", however a pop-up appears saying "ERROR: UCSC library operation failed" and then "connection to server lost!", this never happened before and now it's all I can get for the past 3-4 days. Is there anything I can do to solve it?

Thanks

Hello,

I want to setup a server instance of seqplots on my machine, for the people in my lab to be able to access it.

I setup a shiny server as specified in https://github.com/rstudio/shiny-server
The shiny server seems to work fine

I installed Seqplots:
sudo su -
R
source("http://bioconductor.org/biocLite.R")
biocLite("seqplots")

I tried to follow the instructions in:
http://przemol.github.io/seqplots/#installation---server-deployment
sudo su -
R
library(seqplots)
cp -r $(Rscript -e "cat(system.file('seqplots', package='seqplots'))") /srv/shiny-server/

But:
seqplots(root='/var/shiny-server/DATA')
returns
Error: could not find function "seqplots"

At this stage, the seqplots app cannot be loaded properly and the browser displays:

Running locally the web app seems to work fine:
As normal user
R
library(seqplots)
run()

Could you give me a hand with this issue ?

Thanks for the great work !

Etienne

When trying to create a new plot set, everything works fine with all plot types, except for 'anchored features'.
When I attempt to run calculation with 'anchored features' selected, I receive the following error:

"Error in is.data.frame(x) : object 'M' not found"

I'm using 10bp bins, statistic mean, no additional options, 1000bp upstream, 1000bp anchored, and 1000bp downstream

If I select "Remove zeros", I get the following error:
"Error in M[M == 0] <- NA : object 'M' not found"

If I select statistic = median, I get the following error:
"Error in apply(M, 2, median, na.rm = TRUE) : object 'M' not found"

What is object 'M' and how can I correct for this error?
I'm using version 3.0.12

Hi,

I have multiple bigwig files that are biological replicates. I'd like to plot the mean and error across these replicates (e.g. between bigwigs rather than within each bigwig). Is there a way to do this? I read the manual but I don't see this, maybe I missed it? All the examples only show using 1 bw. As far as I can tell plot() and plotAverage() do the same thing.

Thank you for your help!

Hello,

I'm trying to use seqplots but can't upload any .BED file apparently. Tried with two linked. Didn't work, but a .WIG file was successfully added.
Formation_2018.zip

The errors i have :
at webpage opening : "JavaScript error! Some elements might not work properly. Please reload the page."
Start tutorial > New plot set >"Make sure you have tutorial data uploaded to SeqPlots!" there is no data to plot.
If i try to add a .BED file : "File was not moved to final directory"
Works well when adding a .wig file (attached)

Couldn't try to plot smthing as i don't have any feature file...

Thanks for reading !
Leo

Windows 10 x64
Java version : 1.8.0_171-b11

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252

attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 RColorBrewer_1.1-2 fields_9.6 maps_3.3.0 spam_2.1-4
[6] dotCall64_0.9-5.2 plotrix_3.7 kohonen_3.0.4 BSgenome_1.46.0 Biostrings_2.46.0
[11] XVector_0.18.0 rtracklayer_1.38.3 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0
[16] S4Vectors_0.16.0 RSQLite_2.1.0 jsonlite_1.5 shiny_1.0.5 BiocGenerics_0.24.0
[21] seqplots_1.16.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 lattice_0.20-35 Rsamtools_1.30.0 class_7.3-14 digest_0.6.15 mime_0.5
[7] R6_2.2.2 plyr_1.8.4 ggplot2_2.2.1 BiocInstaller_1.28.0 pillar_1.2.1 zlibbioc_1.24.0
[13] rlang_0.2.0 lazyeval_0.2.1 blob_1.1.1 Matrix_1.2-14 DT_0.4 BiocParallel_1.12.0
[19] stringr_1.3.0 htmlwidgets_1.0 RCurl_1.95-4.10 bit_1.1-12 munsell_0.4.3 DelayedArray_0.4.1
[25] compiler_3.4.3 httpuv_1.3.6.2 pkgconfig_2.0.1 htmltools_0.3.6 SummarizedExperiment_1.8.1 tibble_1.4.2
[31] gridExtra_2.3 GenomeInfoDbData_1.0.0 matrixStats_0.53.1 XML_3.98-1.10 GenomicAlignments_1.14.2 MASS_7.3-49
[37] bitops_1.0-6 xtable_1.8-2 gtable_0.2.0 DBI_0.8 magrittr_1.5 scales_0.5.0
[43] stringi_1.1.7 reshape2_1.4.3 tools_3.4.3 bit64_0.9-7 Biobase_2.38.0 crosstalk_1.0.0
[49] rsconnect_0.8.8 yaml_2.1.18 colorspace_1.3-2 memoise_1.1.0

when I try to make a new plot set, i get the following (error) message and none of the already-loaded tracks display:
Error: The extension ColVis does not exist

Rstudio error log:
Warning: Error in FUN: The extension ColVis does not exist
thanks for the great software - i haven't had any problems with it up until now !

I managed to install seqplots onto my Fedora machine, and run it, but as soon as the seqplot window opens up in Chrome it greys out and is un-clickable. I can not add any files and have to shut it down manually in R.

SeqPlots-3.0.12.dmg on OS X 10.11.6 installs fine, but shows the attached error message on startup.

Hi,

Whenever I run seqplots I am getting an error message
Error in ctx$onInvalidate(function() { :
Reactive context was created in one process and accessed from another

Can you help.
regards,
Amit

thanks for the great software! Only problem I have had is that
I get the following error upon clicking the cluster report button ("clusters indicates"):

error in evaluating the argument 'i' in selecting a method for function '[': Error in !sapply(elementMetadata(gr), function(x) all(is.na(x))) :
invalid argument type

Although pdf downloads work fine from this same toolbar.

Hello, SeqPlot developers!

Your package is very good and easy to use, but it would be very useful to have control over grid and/or ticks for X/Y axes.

can't plot heatmaps (any method). instead i get the following:

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘NSBS’ for signature ‘"list"’

Dear Sir/Madam,

I am trying to use Seqplots for creating a heatmap from BAM files (12) made with HISAT2 and a homo sapiens hg38.91 gtf file. From the first readout it gives me a cannot load vector 3.9 GB and the connection to the server is lost. Can you please advice?

All the best,

Yannis

> BiocInstaller::biocLite("BSgenome.Scerevisiae.UCSC.sacCer1")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 Patched (2016-01-25
  r70000).
Installing package(s) ‘BSgenome.Scerevisiae.UCSC.sacCer1’
installing the source package ‘BSgenome.Scerevisiae.UCSC.sacCer1’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz'
Content type 'application/x-gzip' length 2967322 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'Europe/London'
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'GMT'
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'America/New_York'
* installing *source* package ‘BSgenome.Scerevisiae.UCSC.sacCer1’ ...
Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
Warning in as.POSIXlt.POSIXct(x, tz) :
  unknown timezone 'America/New_York'
** R
** inst
** preparing package for lazy loading
Error in if (file.size(codeFile) == file.size(loaderFile)) warning("package seems to be using lazy loading already") else { : 
  missing value where TRUE/FALSE needed
ERROR: lazy loading failed for package ‘BSgenome.Scerevisiae.UCSC.sacCer1’
* removing ‘/Applications/SeqPlots.app/Contents/Resources/app/Rmac/Versions/3.2/Resources/library/BSgenome.Scerevisiae.UCSC.sacCer1’

The downloaded source packages are in...

sessionInfo()

R version 3.2.3 Patched (2016-01-25 r70000)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocInstaller_1.20.3 tools_3.2.3  

Hi there,

I am trying to import the hg19 reference genome to SeqPlots for my work.

Using the GUI I have been unable to do this. I select the reference genome and then click 'install selected'. A loading bar is then shown at the top of the program but the genome is never installed. I have tried restarting SeqPlots but still had no success.

A friend of mine has had the same issue on MacOS but it was resolved when using Windows, so I believe this is MacOS specific.

Many thanks!

Hi,
I get the following error when I try to upload my wig files.

Processing file: T47D-WT-V_treat_afterfiting_all.wig.gz [8d488f145e4007b7ab315a9d] Error in .Call(get("BWGFile_fromWIG", environment(wigToBigWig)), x, seqlengths(gnm), : Incorrect number of arguments (3), expecting 4 for 'BWGFile_fromWIG'

I thought maybe my wig file is not in format but it's according to the UCSC accepted format. Here is the first ten line if that:
track type=wiggle_0 name="T47D-WT-V_treat_all" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp" variableStep chrom=chr1 span=10 10021 1 10031 1 10041 1 10051 2 10061 3 10071 3 10081 3 10091 7

I would appreciate if you could guide me how I can fix this.
Thanks

Error message:

Warning: file 'publicFiles' has magic number ''
  Use of save versions prior to 2 is deprecated
Error in get(load(file.path("publicFiles", input$publicRdata))) : 
  error in evaluating the argument 'x' in selecting a method for function 'get': Error: restore file may be empty -- no data loaded

Dear Seqplots developers,

I am trying to use the Seqplots 1.12.0 R package.
I am able to upload the bed and bw files but when I try to plot them I always get

Error in ctx$onInvalidate(function()
{ : Reactive context was created in one process and accessed from another

I think this is a shiny of javascript error, but I am unable to figure out by myself.
may you help me?

Session info below

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04

locale:
[1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] RColorBrewer_1.1-2 fields_9.6 maps_3.3.0 spam_2.1-4 dotCall64_0.9-5.2
[6] plotrix_3.7-1 kohonen_3.0.4 BSgenome_1.42.0 Biostrings_2.42.1 XVector_0.14.1
[11] rtracklayer_1.34.2 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 IRanges_2.8.2 S4Vectors_0.12.2
[16] RSQLite_2.1.1 jsonlite_1.5 shiny_1.1.0 BiocGenerics_0.20.0 seqplots_1.12.0

loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.4.0 reshape2_1.4.3 lattice_0.20-35 colorspace_1.3-2
[5] htmltools_0.3.6 yaml_2.1.19 blob_1.1.1 XML_3.98-1.11
[9] rlang_0.2.0 pillar_1.2.2 later_0.7.2 DBI_1.0.0
[13] BiocParallel_1.8.2 bit64_0.9-7 plyr_1.8.4 stringr_1.3.1
[17] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 htmlwidgets_1.2
[21] memoise_1.1.0 Biobase_2.34.0 crosstalk_1.0.0 httpuv_1.4.3
[25] BiocInstaller_1.24.0 class_7.3-14 Rcpp_0.12.17 xtable_1.8-2
[29] scales_0.5.0 promises_1.0.1 DT_0.4 mime_0.5
[33] bit_1.1-13 Rsamtools_1.26.2 gridExtra_2.3 ggplot2_2.2.1
[37] digest_0.6.15 stringi_1.2.2 tools_3.3.2 bitops_1.0-6
[41] magrittr_1.5 lazyeval_0.2.1 RCurl_1.95-4.10 tibble_1.4.2
[45] pkgconfig_2.0.1 MASS_7.3-50 Matrix_1.2-14 R6_2.2.2
[49] GenomicAlignments_1.10.1

Hi, I no longer can use the mac app on 10.14.6, I get:
Error occurred. SeqPlots will terminate.

Starting...
Error in if (!dbListTables(con) == "files") { :
argument has a null lentgh
Moreover : Warning messages:
1: In strptime(x, fmt, tz = "GMT") :
unknown timezone 'zone/tz/2019b.1.0/zoneinfo/Europe/Paris'
2: In strptime(x, fmt, tz = "GMT") : unknown timezone 'GMT'
3: In strptime(x, fmt, tz = "GMT") : unknown timezone 'America/New_York'
4: In dir.create(root) : '/Users/RXC' already exists

I am getting this error during every run of "New plot set" but I can't work out the meaning behind it.

Seqplots v1.10.6 stanalone on Ubuntu 16.04 LTS

Hi,

I am using seqplots to generate aggregate plots. However, different samples are sequenced to different depths. For example, sample1 contains 4x as many reads as sample2. However, in the plot it seems as if it was 2x as many reads. If I normalize the samples by RPM, sample1 even appears to have a lower signal than sample2, even though they are replicates and should overlap. Do you have any comments or ideas on how to normalize sequencing data before subjecting them to seqplots?

Many thanks in advance,
Katrin

Hello,

I'm trying to upload a bed file for a feature, but I keep getting this error: "ERROR: $ operator is invalid for atomic vectors." What am I doing wrong? My bed file looks like this:

chr | start | end | name
chr1 | 101499079 | 101506294 | 5983
chr1 | 101597412 | 101603403 | 5985
chr1 | 102086135 | 102092888 | 5986
chr1 | 102735637 | 102747998 | 5987
chr1 | 102833368 | 102841125 | 5988
chr1 | 103268225 | 103273353 | 5991
chr1 | 103649080 | 103655071 | 5992
chr1 | 103698053 | 103701660 | 5994
chr1 | 103743218 | 103749209 | 5993
chr1 | 104380123 | 104388639 | 5996
chr1 | 104459780 | 104468289 | 5997
chr1 | 104597438 | 104603785 | 5998
chr1 | 105109274 | 105118215 | 5999
chr1 | 108473135 | 108480383 | 6005
chr1 | 109702615 | 109710648 | 6007

Please help. Thanks! Maria

Hi there, I am running on this issue on two laptops with LAN or wi-fi connection. Can you please advice on how to resolve this?

I prefer to use the RStudio console to generate Seqplot heatmaps instead of the GUI. I have not been able to figure out how to return the cluster data after making a heatmap. I see in the manual that I should be able to access a data.frame with clustering assignments and order, but have not been able to do so. Anyone know how to access the clustering data from the console?

Original problem minimal example and illustartion:

plotHeatmap(plotset3, sortrows=FALSE, clusters=5L, main="Peak Regions (clusters=5L)", labels=c("CONTROL","TREATED"), cex.main=20, cex.axis=13, ln.v=FALSE, autoscale=FALSE, zmin=0, zmax=15, clspace= c("yellow","red3"))

Problem affects image function with useRaster=TRUE and grDevices::quartz on Mac OS X (possibly affects grDevices::window and MS Windows as well, not tested). Works fine on x11, pdf, png, etc. Illustrated with minimal example:

data <- matrix(1:10, 10, 10)

dev.new()
par(mfrow=c(1,2))
image(1:ncol(data), 1:nrow(data), t(data), useRaster=FALSE, ylim=c(nrow(data),1), main='useRaster=FALSE')
abline(h=3.5, lwd=4)
image(1:ncol(data), 1:nrow(data), t(data), useRaster=TRUE,  ylim=c(nrow(data),1), main='useRaster=TRUE')
abline(h=3.5, lwd=4)

x11()
par(mfrow=c(1,2))
image(1:ncol(data), 1:nrow(data), t(data), useRaster=FALSE, ylim=c(nrow(data),1), main='useRaster=FALSE')
abline(h=3.5, lwd=4)
image(1:ncol(data), 1:nrow(data), t(data), useRaster=TRUE,  ylim=c(nrow(data),1), main='useRaster=TRUE')
abline(h=3.5, lwd=4)

Hi,

When uploading to Seqplots, I ran into a rather disconcerting problem.
Uploading Bigwig files never fails, it works quite well.
For bed files though, I have to modify the files given to me by the pipeline our bioinformatician uses. I have to first unzip then remove the last 4 columns in excel and then "save as" in text file and I add .bed to the name of the file so that it is recognized as .bed file.
Then the file seems to be recognized as a true .bed file but after a while of "processing", the messages "file was not moved to directory" and sometimes, randomly, 'file could not be renamed" are returned to me. However sometimes after trying to remove a few lanes or renaming the file at some point the file rarely goes through and is accepted and copied. However if I delete it and try to upload the exact same file, it still gives me the same "file was not moved to final directory". So it really seems to be rather randomly (and quite rarely) that the file can be moved, there does not seem to be a problem with the content itself. I have tried copying files locally on my computer, it did not help. Tried checking file permissions, no problem (and no problems with bigwigs that have same properties).
Any idea what could be the problem?

thanks for any help,
best regards

Error occurred. SeqPlots will terminate. I got. error in statement is no such table:files.

Hi,

Another question of mine. I was plotting the same sample around two sets of genes twice, once with 2000 bp flanks and once with 10000 bp flanks. It seems as if the average signal and variance differs even though it is the same data. Can you explain this?

These are my function calls:
getPlotSetArray(tracks="dataset.bw", features=c("genes-class1.bed", "genes-class2.bed"), refgenome="myGenome", xmin=2000, xmax=2000, bin=100)
getPlotSetArray(tracks="dataset.bw", features=c("genes-class1.bed", "genes-class2.bed"), refgenome="myGenome", xmin=10000, xmax=10000, bin=100)

Thanks in advance,
Katrin

Running on Windows 10 with R 3.6.1
Showing the following warning messages from R console.
Calculeating means/stderr/95%CIs...
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
Warning in qt(0.975, sum(!is.na(n))) : NaNs produced
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Exporting results...
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf

When trying to create a heatmap in seqplots I am presented with this error:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘NSBS’ for signature ‘"list"
Could you explain this error to me? do i need to change my table format

Caused by -Inf values when transforming zeros.

I drawed profile plot for five datasets. The inputed bigWig file were created by HOMER and total tag counts were normalized to 1e7. In the profile plot, I noticed the baseline of 5 datasets were quite different (see below). I wonder how the normalization within SeqPlots is done?

Hi,

Not sure if this is a problem with seqplots or whether I am doing something wrong - I'm afraid I'm very new to R...
When I try to upload a file there are no options for genome selection in the dropdown box. If I go to manage reference genomes, there are no genomes available as default and if I try to install one from the available genomes menu. the installation fails. I get the follwing in the R terminal:

Starting...

Data loaction: \icnas4.cc.ic.ac.uk\gaughey/SeqPlots_data

Listening on http://127.0.0.1:3883
2016-09-16 13:13:38 -> Running at http://127.0.0.1:3883, 127.0.0.1 [I10M0SVxgHuqCVyZypuU/w==]
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.4 Revised (2016-03-16
r70336).
Installing package(s) ‘BSgenome.Dmelanogaster.UCSC.dm6’
installing the source package ‘BSgenome.Dmelanogaster.UCSC.dm6’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34147677 bytes (32.6 MB)
downloaded 32.6 MB

'\icnas4.cc.ic.ac.uk\gaughey\SeqPlots_data'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.

• installing source package 'BSgenome.Dmelanogaster.UCSC.dm6' ...
  ** R
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  *** arch - i386
  Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'BSgenome.Dmelanogaster.UCSC.dm6'
  Error: loading failed
  Execution halted
  *** arch - x64
  Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'BSgenome.Dmelanogaster.UCSC.dm6'
  Error: loading failed
  Execution halted
  ERROR: loading failed for 'i386', 'x64'
• removing '\icnas4.cc.ic.ac.uk/gaughey/SeqPlots_data/genomes/BSgenome.Dmelanogaster.UCSC.dm6'
  Warning: running command '"C:/PROGRA1/R/R-321.4RE/bin/x64/R" CMD INSTALL -l "\icnas4.cc.ic.ac.uk\gaughey\SeqPlots_data\genomes" C:\Users\gaughey\AppData\Local\Temp\RtmpCWHxJX/downloaded_packages/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz' had status 1
  Warning in install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome.Dmelanogaster.UCSC.dm6’ had non-zero exit status

The downloaded source packages are in
‘C:\Users\gaughey\AppData\Local\Temp\RtmpCWHxJX\downloaded_packages’

I've tried multiple genomes with the same outcome.
Very sorry if this is a trivial issue that is a result of my inexperience. This looks like just the tool I was looking for, so I am very keen to get it working properly!
Thanks.

I have tried to upload bedgraph files (using the .wig extension as specified) but keep getting the following error message:

Error in adding wiggle: Error in seqlengths(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"character"'
Calls: seqinfo ->

The files are too big to attach here, but the first 10 lines are:

chr1 10007 10011 3.22872
chr1 10011 10037 3.87447
chr1 10037 10051 5.16596
chr1 10051 10099 6.45745
chr1 10099 10120 7.10319
chr1 10120 10126 6.45745
chr1 10126 10141 7.10319
chr1 10141 10145 6.45745
chr1 10145 10209 5.8117
chr1 10209 10222 6.45745

Any help is appreciated.

Hi,
I have Ubuntu 14.04 and installed Seqplots according to the instructions mentioned here:
https://github.com/Przemol/seqplots_electron/releases/tag/v3.0.11.
When I run the file it stops after loading and nothing happens.
The developer tools sections shows this error:
stderr: /tmp/.mount_59BLjw/usr/bin/resources/app/Rlinux/lib64/R/bin/exec/R: error while loading shared libraries: libicuuc.so.55: cannot open shared object file: No such file or directory
There are no libraries by that name for ubuntu 14.04.
Kindly help.

I can run seqplots using R. But I get the following error when using the MacOS package. Thanks.

c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace 'htmltools' 0.3 is already loaded, but >= 0.3.5 is required
In addition: Warning messages:
1: package 'methods' was built under R version 3.2.3
2: package 'BiocGenerics' was built under R version 3.2.2
3: package 'parallel' was built under R version 3.2.3
4: package 'stats4' was built under R version 3.2.3
5: package 'shiny' was built under R version 3.2.3
Error : package or namespace load failed for 'seqplots'

I have installed seqplots on my machine and running through R-studio. I can upload files and create a new plot set (bigwig and bed files) but I don't see a plot preview when I select these. I can create the plots via the pdf function okay.

Thanks for your help.

Hello, I met Julie at the CSH meeting recently and she told me about Seqplots - I just started using it and I have some issues. We would like to analyze strand specific RNA pol II data generated by the CRAC method, which generates (rather large) .wig files.
I tried to add one of our tracks, using the option "custom" for the genome, but this did not work, and I got the following message:

Then I thought that this was due to not having the genome added, so I loaded SacCer3, but again it did not work and I got this message:

Still, my wig file contains the same numbering for the chromosomes, here is the beginning of the file:

It looks like the program has trouble converting the wig to bigwig and this relates to problems with the genome. As a final assay I tried to load our genome, we have it as a .genome package or fasta, but neither appeared as an available genome (the file appeared uploaded, but did not install).
Any suggestion on how to solve these problems ?

Thank you very much
Domenico Libri

Hello,

After generating heatmaps with the clustering I prefer and turning Make cluster calculation repeatable ON when I try to select specific clusters to be plotted I only get the All clusters option. Then reasonably if I try to download cluster information I get the ERROR: Plot heatmap with clusters or ordering first!

I have tried with features files uploaded both as .gff or .bed and signal tracks uploaded as bedgraph.

I am using the latest version of Seqplots 3.0.13 on Windows 7 (64-bit) but I had the same issue with 3.0.12.

Any help would be greatly appreciated.

Kind regards,

Dimitris

Hi,
I would need to scale the y-axis between 0 and 1 on the profiles (modifying the values not just changing the scale).

Is there a way to modify the data? Or could you provide an option for this?

Thank you very much.

Hi, Przemol.

I have successfully uploaded my bigWig and bed data to SeqPlots. When click "new plot set", it just hangs there and reports "processing...". There is no error or warning info in the terminal window. Could you give me some clues? I have installed seqplots in R3.4 before. And now I moved to R 3.5 (a brand-new and not upgraded one) and installed seqplots within it. Will this cause problem?
Thanks.

My session info:

sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /bioware/source/R-3.5.0/lib/libRblas.so
LAPACK: /bioware/source/R-3.5.0/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base

other attached packages:
[1] RColorBrewer_1.1-2 fields_9.6 maps_3.3.0
[4] spam_2.2-0 dotCall64_1.0-0 plotrix_3.7-4
[7] kohonen_3.0.6 BSgenome_1.48.0 Biostrings_2.48.0
[10] XVector_0.20.0 rtracklayer_1.40.6 GenomicRanges_1.32.7
[13] GenomeInfoDb_1.16.0 IRanges_2.14.12 S4Vectors_0.18.3
[16] RSQLite_2.1.1 jsonlite_1.5 shiny_1.1.0
[19] BiocGenerics_0.26.0 seqplots_1.19.3

Hi,

Great tool and a lot of fun to play with. Could you add an option to normalize by total tags? Right now it is very difficult to compare profiles from different size datasets (and the Z-score normalization does not really help)

J