drpowell / fripan Goto Github PK

Avoid confusion with the pan.{html,css} etc files used by the system itself, as we now support multiple pan genomes.

In my browser, the MDS scatterplot is positioned over part of the Fripan image at present. Are other people also experiencing this? I've tried this with google chrome and with safari.

While these colours are much better than the previous collection, with more than 10 colour categories, some of the colours are duplicated, making it impossible to differentiate visually. Is it possible to submit a colours configuration file?

I know this doesn't happen much, but if there is 50 strains and they choose "Order" for "Colour strains" then it pushes everything down.

I wonder if it could be allowed to overflow and overlap the pan genome panel, maybe slightly transparent?

https://github.com/jasonsahl/LS-BSR

Some attributes are continuous (integer wise), not discrete (categories).

Be good if the palette could be switched between distant Brewer to heat map cold to hot.

At the moment you can do pan.html?Foo and it load the Foo.* files.

It would be very helpful for the available pan genomes to be available as a "pull-down" menu in the title bar.

Options:

1. pan.index file with the ones you want to make available in it?
2. static file index.html created by a new fripan tool for managing installations
3. a dynamic index.cgi which scans the folder (assuming they have .cgi enabled)

handle this better?

If we have a column in the .strains file that is an integer that we want to order by, does it work?

Or so we have to ensure zero-padding? eg. 00 01 02 ... 73

after running the command ./server.sh I got the following message:

Run: make compile (or 'make debug' for development) http://localhost:8030/pan.html /home/elliston/miniconda3/bin/python: No module named SimpleHTTPServer

Then, after running the command firefox http://localhost:8030/pan.html, firefox opens with an error page (the one that says unable to connect).

I also cannot visualize the roary data.

Sometimes when i go away and come back it redraws everything back in default green, ignoring my settings for Colouring.

Please create package.json so you don't scare us poor npm n00bs !

npm WARN enoent ENOENT: no such file or directory, open '/Users/torsten/tmp/FriPan/package.json'
npm WARN FriPan No description
npm WARN FriPan No repository field.
npm WARN FriPan No README data
npm WARN FriPan No license field.

Hi David,

could you please tell me which file should I modify to color different groups of genomes. As I understand, I should use pan.strains file, but it doesn't work in my case. I saw the "strain-colour-scheme" was hard-coded as "raw", "cat10", "cat20a", "cat20b", "cat20c" in the pan.html file, so how can I change these values to my own groups.

By the way, is the header "ID Type Order 1 Other" right in the pan.strains file? Is the "1" a typo?

Thanks in advance!

Hello,

I am not sure if I am doing the right thing, I tried to run FriPan but I get this error

ubuntu@anuradhr:~/FriPan$ ./server.sh
Run: make compile
(or 'make debug' for development)
http://localhost:8030/pan.html
Serving HTTP on 0.0.0.0 port 8030 ...
127.0.0.1 - - [17/Apr/2018 08:43:26] "GET /pan.html HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:26] "GET /pan.css HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:26] "GET /build.js HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:26] "GET /pan.index HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:26] code 404, message File not found
127.0.0.1 - - [17/Apr/2018 08:43:26] "GET /pan.proteinortho HTTP/1.1" 404 -
127.0.0.1 - - [17/Apr/2018 08:43:26] code 404, message File not found
127.0.0.1 - - [17/Apr/2018 08:43:26] "GET /pan.roary HTTP/1.1" 404 -
127.0.0.1 - - [17/Apr/2018 08:43:27] "GET /pan.html HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:27] "GET /pan.css HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:27] "GET /build.js HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:28] "GET /pan.index HTTP/1.1" 200 -
127.0.0.1 - - [17/Apr/2018 08:43:28] code 404, message File not found
127.0.0.1 - - [17/Apr/2018 08:43:28] "GET /pan.proteinortho HTTP/1.1" 404 -
127.0.0.1 - - [17/Apr/2018 08:43:28] code 404, message File not found
127.0.0.1 - - [17/Apr/2018 08:43:28] "GET /pan.roary HTTP/1.1" 404 -

Can you please help mw with this. I am tring to run a roary output and I have converted them into FriPan input files.

Many thanks for your help!

Anu

This happens when you change to gene sort to "BY FIRST STRAIN" then back to "INPUT ORDER"

Feature request:

Hi Dave,

After showing this to some collaborators this afternoon they wanted to know if they could remove strains selectively from the MDS plots and dendogram.

Cheers,

Slugger

Hi David,

Is there a way to show the position of a number of genes of interest in the bottom alignment panel, for all strains or selected strains? I know you can show an individual gene (with the large red arrow). I'd like to show a group, from a list, not necessarily a contiguous group. I can't see any way to do that, but thought I'd ask before attempting the javascript, or worse, doing it manually...

Regards,
Liam.

I try to layout test and my data with Chrome and Firefox, but these layout is broken like this;

Also, the descriptions file data is not shonw in scrollable view of the pan genome.

Please tell me how I should solve these problem.

Would like to send a URL with "Order=Clade" and "Colouring=Tolerance" etc to collaborators.

Every page reload re-sets all these.

In the latest version you support a tree lined up with each pan row.

It would be very useful to be able to add the metadata (currenly pan.strains I think) as columns in between the new tree and the pan genome. Each column of metadata should be able to be switched on or off.

                       Year  Country  MLST                            
    +--* ... Sample1   1973    AU     22    xxxxxxxxxxxxxxx
    |
 ---+---* .. Sample2   1984    USA    328   xxxxx xxxx xx
    |
    +-* .... Sample3   1969    UK     3     xxxxxxx  x xx xxxx xxx

eg.

Missing 'Condensation.json', trying deprecated .descriptions file
pan.js:967 Read info on 74.  Columns=Phylo_Order
pan.js:974 Unable to find strain for 2011-14129
pan.js:974 Unable to find strain for 2007-20411
pan.js:974 Unable to find strain for 2006-04017

My .strains file used the ID whereas the .ortho file has ID.faa

Took me over 1 hour to figure out :(

Like this

Would it be possible to search for specific text in the descriptions field?

Great program! However, when I try to layout my data, the MDS plot falls underneath the pangenome plot.

Also, when we have a lot of metadata (.strains columns), mousing over the strain name in the pangenome shows a pop up with all of the metadata but we are unable to see all of it because it goes out of the top of the screen with no way to scroll through it.

https://github.com/sanger-pathogens/Roary

Does browserify need to be -g (global) installed?

This makes it harder for users to install this?
Or does 'global' mean global for user?

We don't seem to use -g for coffeeify etc

I'm npm ignorant.

I receive the following error message after the make compile command:

Compiling src/*.coffee to build.js

browserify -t coffeeify src/main.coffee -o build.js
/usr/bin/env: node: No such file or directory
make: *** [compile] Error 127

I am not very versed in this so am stuck at this stage...

It is true we need to skip over the first 3 columns to get the main matrix.

However, d3.keys seems to be sorting them or changing the input order. It's possible we've gotten lucky for years because our strain names happened to sort ahead of Alg.-Conn. but a numerical strain like 12228 doesn't. See screenshot below.

parse_proteinortho = (tsv) ->
    strains = []
    values = []
    genes = []
    i=0
    for row in tsv
        i += 1
        if i==1
            # DEBUG console.log row
            # DEBUG console.log d3.keys(row)
            strains = d3.keys(row)[3..] # skip first 3 junk columns
                        .map((s) -> {name: s})
            # DEBUG console.log strains.map((s) -> s.name)
        genes.push( {name:"cluster#{i}", desc:""} )
        values.push( strains.map( (s) -> if row[s.name]=='*' then null else row[s.name]) )

    new GeneMatrix( strains, genes, d3.transpose(values) )

Hello,

could You specify how to cite FriPan in article?

Thanks

Hi David.

At the moment, this repo does not come up on a Google search (at least not on the first page), and the repo link in the README file is out of date too.

Cheers.

Anders.

Some real ones would be neat, with metadata.