Comments (8)
nephantes
commented on August 9, 2024
If you use "Choose Dataset" dropdown. You can select all DE genes. For up and down regulated genes. Use up+down. "up" for up regulated "down" for down regulated genes. Since there are many genes in these plots. We have a zooming option. Just use any main plot(scatter, volcano or ma) to select a subset of genes, the selected genes will appear in the next plot. This option reduces mis-click problem.
from debrowser.
lcolladotor
commented on August 9, 2024
Hi,
Hm.. I tried what you describe before submitting this issue. I just tried again.
I ran:
library('debrowser')
startDEBrowser()Selected the demo data. Ran DESeq2. I left the adjusted p-value cutoff at the default of 0.1 and changed the fold change cutoff to 5 so it would be a small list of genes. Although the "choose a dataset" input is already at "up+down", I selected it again. Under the Selected tab, I see nothing although a few genes are colored (yet not manually selected under the Main plots tab). Under the GO term tab, if I click "Submit" I get the following error: unused argument (maxGSSize = maxGSSize).
Best,
Leo
> library(debrowser)
Loading required package: shiny
Loading required package: ggvis
Loading required package: DBI
> startDEBrowser()
Listening on http://127.0.0.1:5122
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
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:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, 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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Warning: Error in enricher_internal: unused argument (maxGSSize = maxGSSize)
Stack trace (innermost first):
81: enricher_internal
80: enrichGO
79: getEnrichGO
78: getGOPlots
77: renderPlot
69: output$GOPlots1
2: runApp
1: startDEBrowser
^C
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.0 alpha (2016-03-23 r70368)
system x86_64, darwin13.4.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2016-03-30
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.3-3.3 2014-11-24 CRAN (R 3.3.0)
annotate 1.49.1 2016-02-06 Bioconductor
AnnotationDbi * 1.33.7 2016-01-29 Bioconductor
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
Biobase * 2.31.3 2016-01-14 Bioconductor
BiocGenerics * 0.17.3 2016-01-29 Bioconductor
BiocParallel 1.5.21 2016-03-23 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
caTools 1.17.1 2014-09-10 CRAN (R 3.3.0)
cluster 2.0.3 2015-07-21 CRAN (R 3.3.0)
clusterProfiler 2.5.6 2016-03-23 Bioconductor
colorout * 1.1-2 2016-03-24 Github (jalvesaq/colorout@f96c00c)
colorspace 1.2-6 2015-03-11 CRAN (R 3.3.0)
DBI * 0.3.1 2014-09-24 CRAN (R 3.3.0)
debrowser * 0.99.0 2016-03-25 Bioconductor
DESeq2 1.11.32 2016-03-27 Bioconductor
devtools 1.10.0 2016-01-23 CRAN (R 3.3.0)
digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
DO.db 2.9 2016-03-30 Bioconductor
DOSE 2.9.6 2016-02-18 Bioconductor
dplyr 0.4.3 2015-09-01 CRAN (R 3.3.0)
DT 0.1 2015-06-09 CRAN (R 3.3.0)
edgeR 3.13.5 2016-03-16 Bioconductor
foreign 0.8-66 2015-08-19 CRAN (R 3.3.0)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
gdata 2.17.0 2015-07-04 CRAN (R 3.3.0)
genefilter 1.53.3 2016-03-23 Bioconductor
geneplotter 1.49.0 2016-01-14 Bioconductor
GenomeInfoDb 1.7.6 2016-01-29 Bioconductor
GenomicRanges 1.23.24 2016-03-09 Bioconductor
ggplot2 2.1.0 2016-03-01 CRAN (R 3.3.0)
ggvis * 0.4.2 2015-06-06 CRAN (R 3.3.0)
GO.db 3.2.2 2016-03-24 Bioconductor
GOSemSim 1.29.2 2016-03-23 Bioconductor
gplots 3.0.0 2016-03-28 CRAN (R 3.3.0)
graph 1.49.1 2016-01-14 Bioconductor
graphite 1.17.1 2016-02-02 Bioconductor
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
GSEABase 1.33.0 2016-01-14 Bioconductor
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
gtools 3.5.0 2015-05-29 CRAN (R 3.3.0)
Hmisc 3.17-2 2016-02-21 CRAN (R 3.3.0)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
htmlwidgets 0.6 2016-02-25 CRAN (R 3.3.0)
httpuv 1.3.3 2015-08-04 CRAN (R 3.3.0)
igraph 1.0.1 2015-06-26 CRAN (R 3.3.0)
IRanges * 2.5.40 2016-03-11 Bioconductor
jsonlite 0.9.19 2015-11-28 CRAN (R 3.3.0)
KernSmooth 2.23-15 2015-06-29 CRAN (R 3.3.0)
lattice 0.20-33 2015-07-14 CRAN (R 3.3.0)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
lazyeval 0.1.10 2015-01-02 CRAN (R 3.3.0)
limma 3.27.14 2016-03-23 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
matrixStats 0.50.1 2015-12-15 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
mime 0.4 2015-09-03 CRAN (R 3.3.0)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.0)
org.Hs.eg.db * 3.2.3 2016-03-24 Bioconductor
plyr 1.8.3 2015-06-12 CRAN (R 3.3.0)
qvalue 2.3.2 2016-01-14 Bioconductor
R6 2.1.2 2016-01-26 CRAN (R 3.3.0)
rappdirs 0.3.1 2016-03-28 CRAN (R 3.3.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.4 2016-03-26 CRAN (R 3.3.0)
reactome.db 1.54.1 2016-03-30 Bioconductor
ReactomePA 1.15.5 2016-02-18 Bioconductor
reshape2 1.4.1 2014-12-06 CRAN (R 3.3.0)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.0)
RSQLite * 1.0.0 2014-10-25 CRAN (R 3.3.0)
S4Vectors * 0.9.44 2016-03-28 Bioconductor
scales 0.4.0 2016-02-26 CRAN (R 3.3.0)
shiny * 0.13.2 2016-03-28 CRAN (R 3.3.0)
SparseM 1.7 2015-08-15 CRAN (R 3.3.0)
stringi 1.0-1 2015-10-22 CRAN (R 3.3.0)
stringr 1.0.0 2015-04-30 CRAN (R 3.3.0)
SummarizedExperiment 1.1.22 2016-03-10 Bioconductor
survival 2.38-3 2015-07-02 CRAN (R 3.3.0)
tidyr 0.4.1 2016-02-05 CRAN (R 3.3.0)
topGO 2.23.3 2016-02-06 Bioconductor
XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
XVector 0.11.7 2016-02-13 Bioconductor
yaml 2.1.13 2014-06-12 CRAN (R 3.3.0)
zlibbioc 1.17.1 2016-03-19 Bioconductor
>from debrowser.
nephantes
commented on August 9, 2024
Selected means, literally selected genes with mouse in the main plots. The list go under selected tab. If you change "Choose Dataset" to selected, you can use those selected genes. On the other hand, up and down regulated genes are used in GO term as a default option. By changing padj, foldchange cutoffs you can change up and down regulated gene lists. The list selected in "Choose Dataset" drop down will be used in GOTerm tab.
from debrowser.
lcolladotor
commented on August 9, 2024
See #15 (comment)
I understand now that the Selected, Up, Down and All Detected tabs are complementary. Just some clarification will be helpful, particularly to understand which genes are used on the GO term tab.
I'll close this issue since it's redundant with #15
from debrowser.
lcolladotor
commented on August 9, 2024
Ahh, I forgot about the unused argument (maxGSSize = maxGSSize) error which I only described in this issue.
from debrowser.
nephantes
commented on August 9, 2024
I don't get this error in my R/3.3.0.
unused argument (maxGSSize = maxGSSize)
I guess, they had updated something after I deposit.
from debrowser.
nephantes
commented on August 9, 2024
Let me know, if you still get this error.
from debrowser.
lcolladotor
commented on August 9, 2024
I ran the same steps I described earlier and did not get an error this time =)
> library('debrowser')
Loading required package: shiny
Loading required package: ggvis
Loading required package: V8
Loading required package: jsonlite
Attaching package: ‘jsonlite’
The following object is masked from ‘package:shiny’:
validate
> startDEBrowser()
Listening on http://127.0.0.1:7465
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
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:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, 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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.0 alpha (2016-03-23 r70368)
system x86_64, darwin13.4.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2016-04-30
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.3-3.3 2014-11-24 CRAN (R 3.3.0)
annotate 1.49.2 2016-04-20 Bioconductor
AnnotationDbi * 1.33.15 2016-04-27 Bioconductor
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
Biobase * 2.31.3 2016-01-14 Bioconductor
BiocGenerics * 0.17.5 2016-04-11 Bioconductor
BiocParallel 1.5.22 2016-04-27 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
caTools 1.17.1 2014-09-10 CRAN (R 3.3.0)
cluster 2.0.4 2016-04-18 CRAN (R 3.3.0)
clusterProfiler 2.99.1 2016-04-10 Bioconductor
colorspace 1.2-6 2015-03-11 CRAN (R 3.3.0)
curl 0.9.7 2016-04-10 CRAN (R 3.3.0)
DBI 0.3.1 2014-09-24 CRAN (R 3.3.0)
debrowser * 0.99.2 2016-04-19 Bioconductor
DESeq2 1.11.45 2016-04-15 Bioconductor
devtools 1.11.1 2016-04-21 CRAN (R 3.3.0)
digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
DO.db 2.9 2016-03-30 Bioconductor
DOSE 2.9.7 2016-04-01 Bioconductor
dplyr 0.4.3 2015-09-01 CRAN (R 3.3.0)
DT 0.1 2015-06-09 CRAN (R 3.3.0)
edgeR 3.13.9 2016-04-20 Bioconductor
foreign 0.8-66 2015-08-19 CRAN (R 3.3.0)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
gdata 2.17.0 2015-07-04 CRAN (R 3.3.0)
genefilter 1.53.4 2016-04-15 Bioconductor
geneplotter 1.49.0 2016-01-14 Bioconductor
GenomeInfoDb 1.7.6 2016-01-29 Bioconductor
GenomicRanges 1.23.27 2016-04-12 Bioconductor
ggplot2 2.1.0 2016-03-01 CRAN (R 3.3.0)
ggvis * 0.4.2 2015-06-06 CRAN (R 3.3.0)
GO.db 3.3.0 2016-04-11 Bioconductor
GOSemSim 1.29.2 2016-03-23 Bioconductor
gplots 3.0.1 2016-03-30 CRAN (R 3.3.0)
graph 1.49.1 2016-01-14 Bioconductor
graphite 1.17.6 2016-04-28 Bioconductor
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
GSEABase 1.33.1 2016-04-27 Bioconductor
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
gtools 3.5.0 2015-05-29 CRAN (R 3.3.0)
Hmisc 3.17-3 2016-04-03 CRAN (R 3.3.0)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
htmlwidgets 0.6 2016-02-25 CRAN (R 3.3.0)
httpuv 1.3.3 2015-08-04 CRAN (R 3.3.0)
igraph 1.0.1 2015-06-26 CRAN (R 3.3.0)
IRanges * 2.5.46 2016-04-17 Bioconductor
jsonlite * 0.9.19 2015-11-28 CRAN (R 3.3.0)
KernSmooth 2.23-15 2015-06-29 CRAN (R 3.3.0)
labeling 0.3 2014-08-23 CRAN (R 3.3.0)
lattice 0.20-33 2015-07-14 CRAN (R 3.3.0)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
lazyeval 0.1.10 2015-01-02 CRAN (R 3.3.0)
limma 3.27.19 2016-04-19 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
Matrix 1.2-5 2016-04-17 CRAN (R 3.3.0)
matrixStats 0.50.2 2016-04-24 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
mime 0.4 2015-09-03 CRAN (R 3.3.0)
miniUI 0.1.1 2016-01-15 CRAN (R 3.3.0)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.0)
org.Hs.eg.db * 3.3.0 2016-04-11 Bioconductor
plyr 1.8.3 2015-06-12 CRAN (R 3.3.0)
qvalue 2.3.2 2016-01-14 Bioconductor
R6 2.1.2 2016-01-26 CRAN (R 3.3.0)
rappdirs 0.3.1 2016-03-28 CRAN (R 3.3.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.4.5 2016-04-16 local
reactome.db 1.55.0 2016-04-20 Bioconductor
ReactomePA 1.15.6 2016-04-27 Bioconductor
reshape2 1.4.1 2014-12-06 CRAN (R 3.3.0)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.0)
RSQLite 1.0.0 2014-10-25 CRAN (R 3.3.0)
S4Vectors * 0.9.52 2016-04-27 Bioconductor
scales 0.4.0 2016-02-26 CRAN (R 3.3.0)
shiny * 0.13.2 2016-03-28 CRAN (R 3.3.0)
shinyjs 0.6 2016-04-25 CRAN (R 3.3.0)
SparseM 1.7 2015-08-15 CRAN (R 3.3.0)
stringi 1.0-1 2015-10-22 CRAN (R 3.3.0)
stringr 1.0.0 2015-04-30 CRAN (R 3.3.0)
SummarizedExperiment 1.1.27 2016-04-27 Bioconductor
survival 2.39-2 2016-04-16 CRAN (R 3.3.0)
tidyr 0.4.1 2016-02-05 CRAN (R 3.3.0)
topGO 2.23.4 2016-04-18 Bioconductor
V8 * 1.0.1 2016-04-04 CRAN (R 3.3.0)
withr 1.0.1 2016-02-04 CRAN (R 3.3.0)
XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
XVector 0.11.8 2016-04-06 Bioconductor
yaml 2.1.13 2014-06-12 CRAN (R 3.3.0)
zlibbioc 1.17.1 2016-03-19 Bioconductorfrom debrowser.
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from debrowser.