Hi

Thanks a lot for the great and cool work.

Is it easy enough to have GeneTonic as a shiny server a la ideal and pcaExplorer

When I do this below within RStudio, a browser does open up with the loaded dataset similar to what you have at http://shiny.imbei.uni-mainz.de:3838/GeneTonic/

library(GeneTonic)
GeneTonic()
example("GeneTonic", ask = FALSE)

Is there a way to replace the datasets etc via the browser - functionalities seen in ideal/pcaExplorer shiny server editions?

Thanks in advance

I have long sample names and when I run gs_heatmap in GeneTonic the column names are cut off from the resulting heatmap. I cannot find the command to adjust the height of the column names, similar to column_names_max_height in ComplexHeatmap. Is there a similar argument to adjust the column name height?

Dear Federico,

I want to apply "GeneTonic" to my dataset. When I used the "get_aggrscores," it returned "NAs" without generating error messages. I have attempted to debug the code but have been unable to identify the root cause of this issue.
I would greatly appreciate your advice on resolving this issue.

Thank you in advance for your help and support.

Best regards,
Anita

It would be nice to have the option to subset the gs_heatmap only to specific samples/conditions.

It would be nice to be able to subset/zoom in the summary heatmap. Maybe we can do someting with ComplexInteractiveHeatmap here?

Hi Federico, i am already enjoying the GeneTonic.

I would like to know if theres is a proper way to export the plotly objects, such as gs_radar graph, as a vectorial image (.svg or .pdf).

Kind regards,
Luciano

Hi,
I just saw your publication in BMC Bioinformatics on GeneTonic, and I would like to say thanks for developing such nice project!

I am playing now with the sample files and code you provided, and everything is working nicely.

In the end I obviously would like to use it with my own data sets. I also analyze datasets for coworkers (that are not very familiar with R/Bioconductor etc). Therefore I was wondering what the best way is to share the interactive GeneTonic output with them. Ideally I would like to send them e.g. the HTML file (+ associated content) so they can interactively explore the results themselves on their own computer. So as a test I naively saved the 'Shiny session' in Firefox as HTML, and then opened it in Chrome, to find out that this is not working...
So, do you have any suggestions on how to do this?

Please note that I don't know anything about Shiny apps.... so it might very well be that (hopefully!) I missed something obvious, or that what I want is rather not possible...

Thanks!
G

The code modal is currently not show in the deployed server

Add a checkbox to enable/disable the labellign of sample names in the Gene Boxplot in the Gene Box

Hi there,
I am writing because I keep finding an error while trying to produce an enrichment_map.
When I call the enrichment_map like this:

emg <- enrichment_map(
  res_enrich = res_enrich,
  res_de = DEseqdata$DESeq2_results,
  annotation_obj = annotation,
  n_gs = 100, #number of gene sets to be considered.
  overlap_threshold = 0.5,
  scale_edges_width = 200,
  color_by = 'gs_pvalue'
)

I get the following error:

Error in `stop_subscript()`:
! Can't subset columns that don't exist.
x Locations 99 and 100 don't exist.
ℹ There are only 98 columns.
Run `rlang::last_error()` to see where the error occurred.

If I type rlang::last_error() I get:

Backtrace:
  1. GeneTonic::enrichment_map(...)
  3. tidyr:::pivot_longer.data.frame(om_df, seq_len(length(gs_to_use)))
  4. tidyr::build_longer_spec(...)
  5. tidyselect::eval_select(enquo(cols), data[unique(names(data))])
  6. tidyselect:::eval_select_impl(...)
 14. tidyselect:::vars_select_eval(...)
 15. tidyselect:::loc_validate(pos, vars)
 16. vctrs::vec_as_location(pos, n = length(vars))
 17. vctrs `<fn>`()
 18. vctrs:::stop_subscript_oob(...)
 19. vctrs:::stop_subscript(...)
Run `rlang::last_trace()` to see the full context.

The majority of the remaining functions do work, so I cannot really explain why this error. Any suggestion would really help!
Thanks
Luca

Hi I'm working on using your package on my own data but I'm running into an issue with the bg_ids object. My dds object and res object look just like the one in the example but when I run my version of res_macrophage_IFNg_vs_naive$SYMBOL <- rowData(dds_macrophage)$SYMBOL I only get the symbols back

Thanks!
Dani

Hi,

I have used the package before and love it but this was on a different computer. I am struggling to install the package because of this error:
Error: object ‘universal’ is not exported by 'namespace:backbone'
Backbone package I have is the latest version 2.1.2

Is there a different version of this package i need to use?

Thanks!

Hi Federico, thanks for your app which can really make my work a lot easier!
For the first time I am approaching RNAseq data analysis and I am adapting my data to the documentation workflow. Once I get to the re_enrich part, when I create bg_ids it returns me a NULL value. How can I solve this problem?
I tried adding the annotation to the dds object but I get no results. I'll write to you below my code.

colData <- read.table('DATI_GeneTonic/samples_table.txt', sep='\t', row.names = 1,header = T)
files <- file.path('DATI_GeneTonic', colData$seqname_quant, "quant.sf")
names(files) <- rownames(colData)
tx2gene <- readRDS("DATI_GeneTonic/tx2gene.gencode.v38.annotation.RDS")
head(tx2gene)

txi <- tximport(files, type="salmon", tx2gene=tx2gene)
ddsTxi <- DESeqDataSetFromTximport(txi,
colData = colData,
design = ~kit+condition)
dds <- ddsTxi
dds$symbol <- mapIds(org.Hs.eg.db,
keys=gene_ids,
column="SYMBOL",
keytype="ENSEMBL")
rownames(dds) <- substr(rownames(dds), 1, 15)
keep <- rowSums(counts(dds)) > 0
dds <- dds[keep,]
dds <- DESeq(dds)
res_control_mutant <- results(dds, contrast = c("condition", "control", "mutant"), lfcThreshold = 1, alpha = 0.05)
res_control_mutant$symbol <- mapIds(org.Hs.eg.db,
keys=ens.str,
column="SYMBOL",
keytype="ENSEMBL",
multiVals="first")
de_symbols_control_mutant <- deseqresult2df(res_control_mutant, FDR = 0.05)$symbol

bg_ids <- rowData(dds)$symbol[rowSums(counts(dds)) > 0]
NULL

Thanks
Marco

Hi Federico,
First of all, thanks for the great package. It is a very useful and interesting tool. Really a great job! Thanks

I was wondering if you could adopt your library to accomodate also people that use edgeR for DE calling. I was thinking maybe at some sort of shake function that would take a DGEList object from edgeR and create a "fake" DEseqResult object, with just the minimal info needed for GeneTonic to work. Would that be possible?

Thanks a lot
Luca

Hi all,

Not so much an issue, but a heads-up that I am experimenting with making a standalone desktop app from GeneTonic using "Electron". People have used this approach to distribute Shiny apps previously without having to setup a Shiny server etc.

e.g.
https://towardsdev.com/converting-a-shiny-app-into-a-standalone-desktop-app-for-windows-ca3656da8468

I don't know if it's common knowledge that Shiny apps can be packaged in this way? Would people be interested in hearing more once I get a working version?

Hi!

I was using GeneTonic, and now I get this message in R:

> library("GeneTonic")

Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio
Error: package or namespace load failed for ‘GeneTonic’:
 object ‘bs4TabPanel’ is not exported by 'namespace:bs4Dash'

And in the bs4Dash I cannot see any package called bs4TabPanel

...
bs4SidebarUserPanel Create a Boostrap 4 dashboard main sidebar
bs4SocialCard AdminLTE3 social card
bs4Sortable BS4 sortable section
bs4Stars AdminLTE3 stars
bs4TabCard Create a Boostrap 4 tabCard
bs4TabItem Boostrap 4 dashboard body
bs4TabItems Boostrap 4 dashboard body
bs4Timeline AdminLTE3 timeline block
bs4TimelineEnd AdminLTE3 timeline block
bs4TimelineItem AdminLTE3 timeline block
bs4TimelineItemMedia AdminLTE3 timeline block
...

Could the package have been renamed?

Hello! I am having issues creating the heatmap that comes with the gs_scoresheat() function and this is because when I run gs_scores() I get the error:

Error in colMeans(thisset_zs) :
'x' must be an array of at least two dimensions

here is the code I'm using:

vst_macrophage <- varianceStabilizingTransformation(kid_dds_trt)
scores_mat <- gs_scores(
se = vst_macrophage,
res_de = kid_res_trt,
res_enrich = res_enrich,
annotation_obj = anno_df
)
gs_scoresheat(scores_mat,
n_gs = 30)

I know this is not the most reproducible problem as you don't have any of the other objects so let me know what else you might need!! Thank you!

GeneTonic shiny app was working fine, but when i tried to make a heatmap following the tutorial the whole R session crashed. I tried updating packages in R and now GeneTonic is broken and I can't reinstall. I get the following error:

library("GeneTonic")

Error: package or namespace load failed for ‘GeneTonic’:
object ‘bs4TabPanel’ is not exported by 'namespace:bs4Dash'

Any help will be highly appreciated. Thanks

I was not able to build the vignette of the package. I also tried to execute each step manually, but it seems like some data is missing.

Hi @federicomarini,

I am wondering if it is possible to compare multiple gene lists in GeneTonic?

Thanks.
Gurpreet

Hi Federico, I would like to know if the gs_horizon is meant to compare enrichment analyses resulting from independent DEG analyses. In my case I am performing three different pairwise comparisons between clones of the same cultivar grown under the same conditions, therefore most enriched processes are shared among the three comparisons.

For each pairwise comparison i have performed independent deseq2 analysis. Afterwards I have performed a geneProfiler analysis, followed by the GeneTonic shaker and aggregate scores functions.

My question is: Is it possible to summarize these three pairwise comparisons into a gs_horizon graph?

I was not able to adapt the instructions shown here: https://federicomarini.github.io/GeneTonic/reference/gs_horizon.html to my datasets..

Thanks in advanced,
Luciano

Hi, I am trying to use GenTonic in our local server, however I am getting the following error which I cannot find a solution for:

> BiocManager::install("GeneTonic")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
Installing package(s) 'GeneTonic'
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GeneTonic_2.0.2.tar.gz'
Content type 'application/x-gzip' length 9023925 bytes (8.6 MB)
==================================================
downloaded 8.6 MB

* installing *source* package ‘GeneTonic’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘universal’ is not exported by 'namespace:backbone'
Execution halted
ERROR: lazy loading failed for package ‘GeneTonic’
* removing ‘/home/user/jmontenegro/R/x86_64-pc-linux-gnu-library/4.2/GeneTonic’

The problem seems to be the object "universal" is not exported, Any suggestions to fix this?

Best regards,

Juan D.

Amazing resource! My JS is a little rusty but would it be possible to create a divergent colorbar that is centred on 0.5 and ranges [0,1]?

I am not sure how to adapt the sprintf JS lines in the function to do that?

When I try the example code below, I got this error "Error in .check_pandoc(ignore_pandoc) : pandoc-citeproc is not available!".

library("GeneTonic")
library("macrophage")
happy_hour(dds = dds_macrophage,
           res_de = res_de,
           res_enrich = res_enrich,
           annotation_obj = anno_df,
           project_id = "examplerun",
           mygenesets = res_enrich$gs_id[c(1:5,11,31)],
           mygenes = c("ENSG00000125347",
                       "ENSG00000172399",
                       "ENSG00000137496")
)

Error in .check_pandoc(ignore_pandoc) : pandoc-citeproc is not available!

I have installed pandoc. But pandoc-citeproc is discontinued. I am using Windows 10. Any suggestions?

> Sys.which("pandoc-citeproc")
pandoc-citeproc 
             "" 

Hi Federico,
Thank you for this really nice and helpful package. It is really useful.
I used it for agronomical species (pig and bovine).
I encountered a problem when trying to use enhance_table function. I have the following error :

p <- enhance_table(res_enrich_pig,

•                res,
  

•                n_gs = 30,
  

•                gtl<-gtl_pig,
  

•                annotation_obj = resannot_Pig,
  

•                chars_limit = 60)
  

Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
les noms de lignes contiennent des valeurs manquantes
I guess the trouble came from the fact that I use ENSEMBLID, convert it in HGNC symbol but as not all genes are identified , I have some missing data (valeurs manquantes in french). Could it be possible to allow missing values in this function ?
Thank you in advance
Regards
Carine