gladstone-institutes / interactive-enrichment-analysis Goto Github PK

Add shiny ui well below each plot with relevant options to allow users to tweak them for viewing and downloading.

Warning: Error in : package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘GO.db’

This error is seen during installation and the same error for 'DOSE' seen in step 1 of 8.

Workaround was to include force=TRUE:

bioc.load.libs <- c(
  "AnnotationDbi",
  "DOSE",
  "enrichplot",
  "clusterProfiler",
  "EnhancedVolcano")
BiocManager::install(bioc.load.libs, force=TRUE)

Some parts of the code assume ORA always with optional GSEA, but that is not the case for gene and rank datasets

I specified in the input that I'm using gene names but keep getting the following error.

Warning in bitr(input$gene, fromType = fromType, toType = toType.list, OrgDb = eval(parse(text = org.db.name))) :
2.28% of input gene IDs are fail to map...
--> No gene can be mapped....
--> Expected input gene ID: 389320,83983,7026,9698,51087,6847
--> return NULL...
Warning: Error in : ‘geneSets’ is not a slot in class “NULL”
8: runApp
7: runUrl
6: shiny::runGitHub
5: eval [C:/Users/LABCU22/AppData/Local/Temp/RtmpEdXVeh/file48453c019a4#28]
4: eval
2: source
1: source_url

E.g.,
<img src="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365454/bin/fnins-13-00025-g0002.jpg" alt="Chronic hyperglycemia impairs neuron function" style="max-height:300px;">

Data tab

• bar plot (Michela)

Results tab

• bar plot

Would users want to skip a particular analysis (e.g., for time) even if their dataset supports it?

We could generate list of radio buttons at the bottom of the Dataset panel for possible methods (given dataset). Users could the deselect methods to skip them.

Hi,

I have been trying to run the analysis using this file EctrlvEKD.csv against the provided human database. However, the analysis gets stuck at step 3:

This also happens if I run the app using one of the example files.
I copied the R studio console log into a word file, attached here
errorlog_IEA.docx

Any help would be appreciated :)

Thanks a lot in advance,

Mariana

I can't reproduce in Chrome 117 or FF.

E.g.,

• use entrezid
• map fold.change (if sig) to color gradient

E.g., User ran analysis on Ensembl, but have a "Gene Name" column. The plot0 options should allow them to display alt column for labels and x-axis.

Have RCy3 ping for Cytoscape.

If not:

• produce friendly message to install and launch Cytoscape; maybe a link to docs with images

If so:

• Open in Cytoscape button for emap and cnet plots (plot1)
• pulldown options (plot2):
  • STRING network (from any gene list)
  • WP data overlay (WP-only)
  • PFOCR data overlay (from NDEX; PFOCR-only)

In plot2, we can show an exported png from Cytoscape, plus offer PDF download.

link to README sections:

• how to cite in side panel
• question mark icons in each panel and tab

Using the example data with default params, when selecting certain pathways (WP) from the results list the WikiPathways plot fails to load for some of the pathways, with an error:

502: Bad Gateway (nginx)

The odd thing is that some pathways that fails from ORA results load just fine from GSEA results from the same run. For example, "spinal cord injury" gives the error for ORA, but not for GSEA. Other pathways give errors for both, for example "PI3K-Akt signaling pathway".

Shouldn't be too hard to distinguish between the few default support types.

For users running via shiny::runGitHub we need to offer some additional download options. This mode of running downloads the repo into /System/Volumes/Data/private/var/folders/pq/w30lpn613x51gjfsdzg3wmg00000gq/T/Rtmp... or thereabouts. Difficult to find and only temporary!

Perhaps the output should always be copied to getwd() to avoid loss of results?

A couple button ideas:

• Save all results --> .tar.gz of output folder
• Share results with shiny app --> .tar.gz of shiny_results folder to allow sharing of explorer tool as well.

when upload Drosophila wikipathways gmt file, building new database process is too long and seems never get ready.

Hi,

I have problem in launching the app.

if(!require(devtools)) install.packages("devtools"); library(devtools)
options(shiny.launch.browser = .rs.invokeShinyWindowExternal)
source_url("https://raw.github.com/gladstone-institutes/Interactive-Enrichment-Analysis/main/launch_app.R")
SHA-1 hash of file is "0d4c9db604af8a7751914b83bb92161ce4538002"
[1] "All initial libraries successfully installed and loaded."
Downloading https://github.com/gladstone-institutes/Interactive-Enrichment-Analysis/archive/HEAD.tar.gz
Error in utils::download.file(url, method = method, ...) :
download from 'https://github.com/gladstone-institutes/Interactive-Enrichment-Analysis/archive/HEAD.tar.gz' failed
In addition: Warning messages:
1: In utils::download.file(url, method = method, ...) :
downloaded length 0 != reported length 0
2: In utils::download.file(url, method = method, ...) :
URL 'https://codeload.github.com/gladstone-institutes/Interactive-Enrichment-Analysis/tar.gz/1e9ced583814957f780cea0c0d855f625a27e576': Timeout of 60 seconds was reached

Could you give me some idea to solve this problem?

Thank you so much!

If more than one dataset in run, then add top-level drop-down in Results tab to "Compare with..." another dataset result, plus another drop-down for "Union" or "Difference" (A vs B; offer icon to swap set order).

• Changes table (per db) to a union or setdiff listing with A/B geneLists. Display concatenated stats or new stats about intersection?
• Plot1 remains the same, plus add a new heatmap: datasets (row) vs top n union terms (columns) [maybe always include this plot for all datasets when more the one? And limit to A/B pair iff "Compare with..."?]
• Plot2 remains the same, with diff (A) genes highlighted or with 3-color code for A/B/union genes

add if statement to skip plots if no results

To limit display (and plots) to sig results. Checked by default?

It is stuck at step 3 and cannot continue

Downloading https://github.com/gladstone-institutes/Interactive-Enrichment-Analysis/archive/HEAD.tar.gz

Listening on http://127.0.0.1:4791
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29 ucrt)
Installing package(s) 'AnnotationDbi', 'DOSE', 'enrichplot', 'clusterProfiler',
  'rWikiPathways', 'EnhancedVolcano', 'org.Mm.eg.db'
Warning: packages ‘AnnotationDbi’, ‘DOSE’, ‘enrichplot’, ‘clusterProfiler’, ‘rWikiPathways’, ‘EnhancedVolcano’, ‘org.Mm.eg.db’ are in use and will not be installed
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(input$gene, fromType = fromType, toType = toType.list, OrgDb = eval(parse(text = org.db.name))) :
  5.46% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(input$gene, fromType = fromType, toType = toType.list, OrgDb = eval(parse(text = org.db.name))) :
  5.46% of input gene IDs are fail to map...
Warning in gzfile(file, mode) :
  cannot open compressed file '..//../shiny_result/output/20240319_102038/TopGenesClus5Macro/ora/TopGenesClus5Macro_go_mm_20240315_ora_geneList.rds', probable reason 'No such file or directory'
Warning: Error in gzfile: cannot open the connection
  8: runApp
  7: runUrl
  6: shiny::runGitHub
  5: eval [C:/Users/moham/AppData/Local/Temp/RtmpeSBCDh/file6928298968c3#28]
  4: eval
  2: source
  1: source_url

• uninstall all libs
• add docs for installing initial set of libs (e.g., shiny)

Can't take -log10(0) when calculating rank.

Solution: replace 0's with p.value < min(p.value) in datasets.

1. In the launched RShiny app, when I select the Mm_20231016.RData database and then select the provided E-GEOD-30573.csv dataset, the "Choose organism" dropdown is "human". Screenshot below. Is this expected? Shouldn't it auto populate based on the database that was picked and be "mouse" and not "human" in this scenario?

2. For the Mm_20231016.RData database and E-GEOD-30573.csv dataset, the dot plot and concept network in the results tab shows an error. Is this expected? Also, do you think it might be useful to handle such errors in the background and show a message like "An error has occurred while running this operation. Contact <point_of_contact> for further assistance." ? I can work on adding this functionality.
   

3. The “Let’s go!” button is on the left menu bar. After selecting the database and dataset, it is not immediately intuitive to look for that button. A message to ask the user to click the button would be helpful. Placing the button on the screen and not just in the bar might help if the menu bar is closed and will also be easier to find.

4. For the Hs_20231016.RData database; E-GEOD-30573.csv dataset and default options, I have a few questions about the results screen:

   4a. There is a collapsible "Summary" text box with blank fields. Should this be removed?

   4b. In the results tab, when "pfocr_hs_20231016" database is selected, the PFOCR image is broken.

   4c. In the results tab, when "pfocr_hs_20231016" database is selected, the names of pathways are overlapping in the "Choose a plot type for top results:" for most of the plots.
   

   4d. In the results tab, when"pfocr_hs_20231016" database is selected, in the Concept network plot in the results tab, the dot sizes are hidden as the plot options overlap the dot sizes.
   

• upload GMT files
• read and verify GMTs
• generate RDATA
• select RDATA