caleydo / lineup Goto Github PK

[DEPRECATED] Caleydo LineUp using the LineUp.js library --> use https://github.com/Caleydo/lineup_app instead

License: BSD 3-Clause "New" or "Revised" License

JavaScript 48.28% HTML 15.91% TypeScript 33.78% CSS 1.19% Dockerfile 0.84%

lineup's Introduction

Caleydo - Visualization for Molecular Biology

Caleydo is a visualization framework for molecular biology data. It is targeted at analyzing multiple heterogeneous but related tabular datasets (e.g., mRNA expression, copy number status and clinical variables), stratifications or clusters in these datasets and their relationships to biological pathways.

For user documentation please refer to the Caleydo Help. For general information and downloads based on binaries please use the Caleydo Website. This guide assumes that you want to install Caleydo from source.

Installation

Caleydo uses Java, OpenGL and the Eclipse Rich Client Platform (RCP). Things you need to install before being able to run Caleydo:

Eclipse Kepler for RCP and RAP Developers, which you can get from the eclipse download page. Other Eclipse versions won't work.
Install EGit in Eclipse using software updates.
Java SDK >= 1.7

To install Caleydo use EGit within Eclipse and clone the repository. Each directory in the caleydo-dev folder corresponds to an Eclipse project. Here is a good tutorial on how to import Eclipse projects from git.

If you want to use ssh (instead of https) for communicating with github out of eclipse follow these instructions. You will have to generate a new RSA key and save it to you ~/.ssh folder. Remeber to set a passphrase for you key. This will result in a file ida_rsa and ida_rsa.pub turning up in your ssh folder. Save your public rsa key with your eclipse account folder.

When cloning the repository follow the above tutorial. Don't change the username "git" to your username!

Team

Caleydo is an academic project currently developed by members of

Institute for Computer Graphics and Vision at Graz University of Technology, Austria
Institute of Computer Graphics at Johannes Kepler University Linz, Austria
Pfister Lab at the School of Engineering and Applied Sciences, Harvard University, Cambridge, USA
Park Lab at Harvard Medical School, Boston, USA

Acknowledgements

Caleydo makes use of a range of open source tools, bioinformatics resources and pre-packages several datasets, which we gratefully acknowledge here.

Software Libraries

Bubble Sets - A Java implementation of the visualization technique.
CDK - The Chemistry Development Kit.
JGrahT - A graph library.
Jogl - Java bindings for OpenGL.
PathVisio - loading and parsing WikiPathways.
WordHoard - statistical utilities.

Bioinformatics Resources

David Bioinformatics Resources - Gene ID mapping.
KEGG - Pathways.
WikiPathways - Pathways.

Datasets

CCLE - BROAD Institute Cancer Cell Line Encyclopedia.
TCGA - The Cancer Genome Atlas.

Resources

GitHub - Hosting our source code.
WebStorm - Free developer licenses for our web projects from JetBrains.

lineup's People

Contributors

Stargazers

Watchers

Forkers

bikramkawan

lineup's Issues

Add link to data source for demo datasets

Caleydo/lineupjs#101

Support matrix data on import

Identify matrix data and select Matrix column data structure

dropbox data support

e.g. via https://www.dropbox.com/developers/dropins

Caleydo/lineupjs#61

Enable direct NPM install from github

Release number or git hash: 53b52eb (latest on taggle branch)
Web browser version and OS: NA
Environment (local or deployed): Docker

Steps to reproduce

Since there's a package.json at the top level, I think we should be able to npm install from github?

Dockerfile:

FROM python:3.6.3
# TODO: Use Node base image. Getting an error right now:
# Step 1/5 : FROM node:9.7.1 AS build
# Get https://registry-1.docker.io/v2/library/node/manifests/9.7.1: unauthorized: incorrect username or password
# .... but this isn't the problem I'm filing this issue for: Just ignore. 

RUN apt-get update && \
    apt-get install -y npm

# Pick another github npm project at random to demonstrate that it works:
RUN npm install toddmotto/angular-component
# But this doesn't:
RUN npm install caleydo/lineup\#53b52eb

produces:

npm WARN package.json [email protected] No repository field.
npm WARN engine [email protected]: wanted: {"npm":">= 3","node":">= 6","iojs":">= 3"} (current: {"node":"0.10.29","npm":"1.4.21"})
npm ERR! 404 Not Found
npm ERR! 404 
npm ERR! 404 'types/file-saver' is not in the npm registry.
npm ERR! 404 You should bug the author to publish it
npm ERR! 404 It was specified as a dependency of 'lineup'
npm ERR! 404 
npm ERR! 404 Note that you can also install from a
npm ERR! 404 tarball, folder, or http url, or git url.

npm ERR! System Linux 4.9.49-moby
npm ERR! command "/usr/bin/nodejs" "/usr/bin/npm" "install" "caleydo/lineup#53b52eb"
npm ERR! cwd /
npm ERR! node -v v0.10.29
npm ERR! npm -v 1.4.21
npm ERR! code E404
npm ERR! git clone [email protected]:github:Caleydo/lineupjs Cloning into bare repository '/root/.npm/_git-remotes/git-github-com-github-Caleydo-lineupjs-167d2368'...
npm ERR! git clone [email protected]:github:Caleydo/lineupjs Host key verification failed.
npm ERR! git clone [email protected]:github:Caleydo/lineupjs fatal: Could not read from remote repository.
npm ERR! git clone [email protected]:github:Caleydo/lineupjs 
npm ERR! git clone [email protected]:github:Caleydo/lineupjs Please make sure you have the correct access rights
npm ERR! git clone [email protected]:github:Caleydo/lineupjs and the repository exists.
npm ERR! git clone [email protected]:github:phovea/phovea_core Cloning into bare repository '/root/.npm/_git-remotes/git-github-com-github-phovea-phovea-core-4c7d6d73'...
npm ERR! git clone [email protected]:github:phovea/phovea_core Host key verification failed.
npm ERR! git clone [email protected]:github:phovea/phovea_core fatal: Could not read from remote repository.
npm ERR! git clone [email protected]:github:phovea/phovea_core 
npm ERR! git clone [email protected]:github:phovea/phovea_core Please make sure you have the correct access rights
npm ERR! git clone [email protected]:github:phovea/phovea_core and the repository exists.
npm ERR! git clone [email protected]:github:phovea/phovea_ui Cloning into bare repository '/root/.npm/_git-remotes/git-github-com-github-phovea-phovea-ui-b9a6620b'...
npm ERR! git clone [email protected]:github:phovea/phovea_ui Host key verification failed.
npm ERR! git clone [email protected]:github:phovea/phovea_ui fatal: Could not read from remote repository.
npm ERR! git clone [email protected]:github:phovea/phovea_ui 
npm ERR! git clone [email protected]:github:phovea/phovea_ui Please make sure you have the correct access rights
npm ERR! git clone [email protected]:github:phovea/phovea_ui and the repository exists.
npm ERR! git clone [email protected]:github:phovea/phovea_importer Cloning into bare repository '/root/.npm/_git-remotes/git-github-com-github-phovea-phovea-importer-899439f9'...
npm ERR! git clone [email protected]:github:phovea/phovea_importer Host key verification failed.
npm ERR! git clone [email protected]:github:phovea/phovea_importer fatal: Could not read from remote repository.
npm ERR! git clone [email protected]:github:phovea/phovea_importer 
npm ERR! git clone [email protected]:github:phovea/phovea_importer Please make sure you have the correct access rights
npm ERR! git clone [email protected]:github:phovea/phovea_importer and the repository exists.
npm ERR! 
npm ERR! Additional logging details can be found in:
npm ERR!     /npm-debug.log
npm ERR! not ok code 0

Expected behavior

npm install caleydo/lineup#taggle has no errors.

Mark guessed columns

Columns that are imported (without import dialog) should get a visual marker/flag. You have to change the lineupjs library.

Restore from Gist broken

@mstreit commented on Fri Nov 10 2017

Release number or git hash: deployed
Web browser version and OS: chrome

Steps to reproduce

save to gist
take link and past it in second browser window

Observed behavior

Only one item is contained in the restored table.

Expected behavior

Same items as in stored table.

Add group and aggregation column after import dataset

Add the group and aggregation column ...

... to the column chooser
... as default column (next to the rank)

Demo gets stuck at loading icon

No interaction possible because of loading icon overlay.

https://sgratzl.github.io/lineup_demos/

Here is what I get in Chrome:

Column texture renderer

User switches to the texture overview (#36)
current rows (from detail mode) must be hidden
Render a texture of all rows as image
Place this texture image to column

downloaded file is named incorrectly

migrated from Caleydo/lineupjs#164

Reproduce

go to https://sgratzl.github.io/lineup_demos/#
upload new file
export file to CSV using the arrow-to-disk-button

Observed

downloaded CSV file is named after the previously loaded data set (here the default data set that loads when visiting above URL)

Expected

downloaded CSV named after the uploaded file

Generate test CSV data using Ordino

Go to http://ordino.caleydoapp.org
Load all genes
Add single score columns
Add aggregated score columns (as raw matrix)
Download CSV

Upload the generated CSV data to Google drive.

Broken CSV import in Taggle

Release number or git hash: 8faec24
Web browser version and OS: Chrome v64
Environment (local or deployed): both

Steps to reproduce

Open Taggle
Click the file import button (from the header)
Select a CSV file
Click Import

Observed behavior

The importer throws the following error message:

importer.ts:114
Uncaught TypeError: buildCSV is not a function
    at Object.getResult (importer.ts:114)
    at HTMLButtonElement.<anonymous> (importer.ts:126)
    at HTMLButtonElement.dispatch (jquery.js:5201)
    at HTMLButtonElement.elemData.handle (jquery.js:5009)

Expected behavior

Lineup/Taggle should import and show the data

Error handling on parse error

When importing a dataset/file that is not supported an error dialog should open. You can use the generateDialog() function from the importer.

Switch column type after import

At the moment the user chooses the column type in the import dialog. When we import data directly we have to allow the user to switch column types after import (e.g., if categorical is a string, etc.).
This should be done on click on the visual marker (see #25).

use FileSaver.js for saving files

see https://github.com/eligrey/FileSaver.js/

Highlight detail area in texture overview

Selected rows should be highlighted in the texture overview. We could use the line of the aggregation column and draw the locations in orange.

Replace Taggle overview with new texture overview

Turn off live Taggle overview rendering
Use texture renderer overview instead (#35)

Matrix stratification not restoring correctly from Gist

@katush commented on Mon Nov 20 2017

Matrix stratification not restoring correctly from Gist. Although the stratification is there, each stratified column contains all the matrix data (1990-2015) instead of 1990-1999, 2000-2010, 2010-2015.

There were also missing stratification data for matrices when I tried to re-add and re-stratify them:

Direct link to demo datasets with hashtags

Caleydo/lineupjs#100

tweet direct link to demo datasets with hashtags that make the respective target audience aware of the demo.

Use colors of original LineUp

Caleydo/lineupjs#65

JavaScript error: cat is undefined

class: CategoricalColumn
method: initCategories

Taggle branch does not build (locally and on AWS)

Locally:

WARNING in ./src/app.ts
42:21-27 "export 'default' (imported as 'Taggle') was not found in 'lineupjs/src/taggle'

ERROR in [at-loader] src/app.ts:14:8
    TS1192: Module '"/Users/marcstreit/phovea/lineup/node_modules/lineupjs/src/taggle"' has no default export.

Remote:
https://circleci.com/gh/Caleydo/lineup_product?utm_campaign=chatroom-integration&utm_medium=referral&utm_source=slack

@thinkh, any ideas what the problem could be?

first four columns should be frozen

@mstreit commented on Mon Sep 11 2017

all columns until label column should be frozen (not impacted by horizontal scrolling).

@alexsb commented on Mon Sep 18 2017

More generally, I want to define columns that shouldn't scroll form the left, as is possible in google spreadsheets.

caleydo / lineup Goto Github PK

lineup's Introduction

Caleydo - Visualization for Molecular Biology

Installation

Team

Acknowledgements

Software Libraries

Bioinformatics Resources

Datasets

Resources

lineup's People

Contributors

Stargazers

Watchers

Forkers

lineup's Issues

Steps to reproduce

Expected behavior

Steps to reproduce

Observed behavior

Expected behavior

Steps to reproduce

Observed behavior

Expected behavior

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