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View Code? Open in Web Editor NEWamica: an interactive and user-friendly web-based platform for the analysis of proteomics data
License: GNU General Public License v3.0
amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
License: GNU General Public License v3.0
Feature request:
Add the option to download the underlying heatmap data.
Dear Sebastian and amica team,
Thanks again for all your work to make this useful tool publicly available.
I understand that the imputation is necessary for some of the features in amica, however this may affect the analysis for some of the proteomics data. This includes the analysis of the IP samples, where the bait protein and some potential binders are only present in one group. Or the proteomic analysis of the samples with the knockout genes. Is there any options in amica to count for these cases?
Can we have a new feature to generate new plots (maybe Venn?) for the samples before imputation?
Thanks
Hello,
I've encountered an issue where an "X" prefix gets added to sample names when I upload the experimental design file.
Below is a screenshot from the original .txt file, where the sample names don't have the "X" prefix:
However, when uploaded to the amica server, the "X" prefix appears:
Is there any workaround for this issue? The prefix also gets carried over to the graphs, which is not ideal.
Thank you for your assistance!
Hi I am trying to analyse my data from MQ and getting the following error "error in limma Error in names(x) <- value: 'names' attribute [2] must be the same length as the vector [0]" could you please tell me what the problem could be?
Also, the example files are in .csv format and Amica asks for tsv files. Is it possible to change that?
Hello,
I encountered an error when trying to generate a heatmap using the "Differential Abundance" tab.
Steps to Reproduce:
After pressing "Submit", it gave two errors:
a) in the UI:
Error: NA/NaN/Inf in foreign function call (arg 10)
b) in the cmd:
Warning: Error in hclustfun: NA/NaN/Inf in foreign function call (arg 10)
107: %||%
104: modify_list
103: config
101: renderPlotly [\amica\amica/server.R#1571]
100: func
97: shinyRenderWidget
96: func
83: renderFunc
82: output$compareHeatmap
1: runApp
The "Download heatmap data" function appears to work correctly. However, upon inspection of the downloaded data, there are several NA values present in the table. This might be related to the error encountered.
Regards,
Bola
Hi,
I've been using Amica successfully, but I've got a set of samples where I can't get it to work. I keep checking the names of the columns in the DIANN pg matrix to make sure the spellings all match what's in the design and contrast files, but I can't get past this error that halts everything as soon as I press "upload". Some function is failing to get one of its arguments, but I don't know how to trace back to see where the problem is.
Here's the error I get:
"Warning: Error in paste0: argument is missing, with no default"
Any thoughts?
Thanks,
Noah Dephoure
I just wanted to quickly express my gratitude for your great tool. I really enjoy using is.
I would only like to suggest to enable different types of depicting protein profile plots across several samples. It would be great if you could enable to depcit all individaul data points in each sample. Another great way to depcit the profile plots, would be via violin plots.
For getting a large user base, I think it would be good for this tool to function indepentently on Rstudio etc. I am a little familiar with non R coding and was suffering/troubleshooting a lot to get it running and feel this may be a high entry barrier for people.
Howver, I think it was worth it ;)
Cheers
Hi Sebastian,
Is it possible to implement another significant cutoff other than the ones available? It is called Xiao correction. Here is the link to the paper.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957066/
Thanks
Maithy
Hi Sebastian,
I was asked by a user of Amica if it would be possible to add an additional protein selection option to the Volcano plot in the "Differential abundance" tab? Specifically, it would be useful to have the option to manually submit a list of protein identifiers (Uniprot IDs, Gene names, ...), which are then highlighted and labeled in the volcano plot, similar to what is happening if you use the selection tool. Optimally, the highlighted dots would be plotted above the other points and highlighted with a different color.
Please let me know if it is possible to add this feature.
Best,
David
Is this software compatible with Fragpipe TMT experiments?
This issue was already resolved, see (#15).
But somehow the functionality on the server is completely broken when this fix was applied, hence the version on the server does curr. not support FragPipe v18 output yet.
This does not effect the code on github, running locally should work without issues!
Hopefully, this will be soon resolved. Something must have gone wrong with docker build, the code seems fine.
The full functionality is back again on the public server. Very sorry!
Best,
Sebastian
Hello,
During a recent data analysis, I observed that the RawIntensity
values in the exported amica file are identical to the ImputedIntensity
values. This occurred after a run with vsn normalization and no imputation.
Steps to Reproduce:
RawIntensity
and ImputedIntensity
.I suspect this behavior might be a bug. Would you be able to provide clarification or confirm the issue?
Kind Regards, Bola
Hello,
I encountered an error when trying to generate a dotplot in the "Differential Abundance" tab.
In the UI: it shows in red: Error: 'list' object cannot be coerced to type 'double'
In the cmd:
Warning: Error in dist: 'list' object cannot be coerced to type 'double'
171:
170: stop
169: dotplot
168: renderPlot [\amica\amica/server.R#1174]
166: func
126: drawPlot
112: reactive:plotObj
96: drawReactive
83: renderFunc
82: output$dotplot
1: runApp
Thanks for your help.
Regards,
Bola
Dear amica developer team,
Thank you for developing this really useful tool. The design and implementation of the shiny app is nicely done.
Have you tested amica for DIA data? In particular, I am interested in analyzing DIA output from Spectronaut.
Thanks
Hello,
I am trying to analyse data using amica: DIA. I uploaded the .pg matrix and design and contrast file in the required format. However, I keep getting error the names of my samples doesn't match in input file and design file. I have tried several times by changing the names as well. Could you please help me where I am going wrong? I have attached the files from two trials (sample names are different in boh the trials). I changed the pg matrix file to .txt as I cannot upload .tsv file here.
contrasts_trial1.txt
design_trial1.txt
contrasts_trial2.txt
design_trial2.txt
[report.pg_matrix.tsv__trial2.txt](https://github.com/tbaccata/amica/files/15292070/report.pg_matrix.ts
report.pg_matrix_trial1.txt
v__trial2.txt)
Thank you
Hi, I would like to use Amica for my proteomic data.
However, when I uploaded my files, the screen changed to grey and does not move from there.
So, I tried to run Amica from R and there was an error message like below.
Warning: Error in $<-.data.frame: replacement has 0 rows, data has 48
Could you tell me what I did wrong?
Kind regards,
J.
Hi, when running the app on RStudio I get the following warning "Warning in is.call(funBody[[idx]]) && as.character(funBody[[idx]][[1]]) == :
'length(x) = 3 > 1' in coercion to 'logical(1)'" repeatedly in the console and I can't visualize the table with the differentially expressed proteins, but all the figures are produced normally. Could you help solving this issue?
Thanks
Hi,
Firstly let me say i think this tool looks amazing. I am struggling a bit with the input formats however. I have an output from DIA-NN (report.pg-matrix.tsv), which contains proteinID, gene name and LFQ intensity for my runs. I have formatted this into the format required for custom file upload, including a specifications file to let amica know my headers. When i click analyze, i get a small popup in the right corner saying "no data uploaded". I am not sure what to make of this (amica reports upload complete when i add the proteingroups.txt and other files).
I would process with fragpipe or something else if that was easier, but to my knowledge fragpipe does not yet support DIApasef data.
Thanks in advance
Silas
Implement Dot plots, from https://prohits-viz.org/help/analysis/dotplot:
Dot plots have the advantage over heat maps in that they use the same amount of space but visualize more information. In addition to raw quantitative values being displayed via coloured circles, dot plots display the relative readout measurement between conditions via circle size and confidence in the measurement via coloured edge. Heat maps, however, are better for presenting very large data sets as the detailed information of a dot plot gets lost in these instances.
Things to consider
Hi,
I managed to upload correctly data from DIA-NN but when I click on analyze the app crashes and the console prints the following error
Warning: Error in :: argument of length 0
Is there anything I'm missing?
Thanks
Lucio
Hello and great work on this tool! Hope that you are able to get this published very soon :)
I would like to request a new feature for the enrichment analysis. Could you please have the genes from the input that are associated with each enrichment term be output in a column in the output table? This would be great to know which genes are the reason for a certain enrichment.
Thanks!
Hello,
Thank you for developing this tool. I am using FragPipe output. I used to be able to use it but now I am stuck on a faded grey page after clicking on Analyze both on the web version and the R version. On the R version, in the terminal, this error is displayed Warning: Error in [[: attempt to select less than one element in get1index 1: runApp
Could you help please ?
Thank you in advance for your help.
Input file firsttwolines.txt
Contrast file contrast.txt
Design file design.txt
Hi Sebastian,
I have a custom output file from DIA-NN. It seems to be getting uploaded successfully but when I press analyze it says no data uploaded. I have attached the files here. Could you please tell me what could be the problem?
Thanks
Maithy
amica_groups.txt
amica_specification.txt
Pel_Amica_Example.txt
amica_expt.txt
Hello,
when trying to upload DIA-NN output, this error pops up:
"simpleWarning in readLines(inFile$datapath, n = 1): line 1 appears to contain an embedded nul"
How to fix it?
Thanks
Hello again,
I just wanted to report a minor bug, which I've encountered: It's not possible for me to label individual proteins in the QC correlation dot plots. I can use the selection tools, however no labels appear.
Suggestion (not demand :D):
In regards to the volcano plots, it would be really nice if it was possible to fix labeled protiens in the volcano, so that it's possible to fine tune the labeling.
Best
Andree
Hello,
I am using Amica for the first time. I've uploaded my data (QC'ed MetaMorpheus output) using the custom format option as well as the experimental design, contrast matrix, and specification file. However, after hitting upload I do not get an error and the application appears to be frozen. It is unclear if it is running and even after several hours looks the same. Can you please advise?
Thank you.
Add option to choose only quantified proteins as background gene list in over-representation analysis.
By default, all protein-coding genes are considered as background.
HI,
I have t output from DIA-NN, would you able to help for correct formatting.
Protein.Group | Protein.Ids | Protein.Names | Genes | First.Protein.Description | 388 | 399 | 404 | 405 | 407 | 408
388 _Control
399_Control
404_Control
405_KO
407_KO
408_KO
Best,
Hi, everything works nicely for me and I find amica outstanding, only thing I can't produce is heatmaps. For some reason I get this error "Not all levels of the column_side_colors are mapped in the column_side_palette. Could you help with this?
Thanks a lot!
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