Getting D3 static tree diagrams by using force layout - d3.js

Please help me create diagrams like these: (I tried, but stuck on setting up force layout)
Here is an implementation of ordinary D3 tree with "FISH" data:
The challenge is: How do we get diagram below from diagram above? (but without "hardcoding" of coordinates; this means, there is a need for applying force layout, or similar method)

Complete tutorial can be found here.
You should also read documentation for tree layout.

Related

d3.js Search functionality in collapsible tree

I have created my visualization similar to the http://mbostock.github.com/d3/talk/20111018/tree.html. I wish end users to be able to search for node/data/label from the tree. Since I am not good with javascript I am finding quite hard to create such search functionality.
Here are my requirements: End users can type text like 'cluster' (flare->analytics-->cluster) and type enter. The visualization highlights cluster and shows to the end users.
If it is possible could you share the code using jsfiddle?
Not sure if this question is still valid but a D3 node tree version that I found that really helped is this one:
Jake Zieve's "Search Collapsible Tree
Let me know if this helps. The code should be pretty similar to the one you attached. Either way, let me know if this will lead you on the right path.

Modifying d3js parsets reusable chart

I am new to D3js and working with the parsets reusable chart (http://www.jasondavies.com/parallel-sets/). I want to make changes to this chart such as adding sort based on thickness of ribbons on mouseover, and overlaying two parallel sets over each other to compare different datasets at once (The one at the back being faded).
Being new to D3js, I am having difficulty in understanding where to start. I am currently trying to understand the code of d3.parsets.js but its not going too well. If anyone has worked with this before and understands the procedure being followed in the code, please help me out.
The best adaptation I've seen of d3.parsets.js is by Hongjian Yang: Airline Vis adapted from d3.parsets.
It may be able to accomplish some of what you're looking for, though I'm not sure you'll readily be able to overlay two datasets (nor am I sure I understand the need to do so).

Masonry algorithm for d3.js

Is there a masonry type algorithm for d3.js? (a la isotope http://isotope.metafizzy.co/)
As a related question (if that's not available), how would I go about doing it? Specifically: I know the enter/update/exit paradigm of d3, but it seems like it treats all the points independently of each other. If I wanted to change the layout of the 2nd point, based on where I put the 1st point, how would I do that?
The matrix layout might be what you are looking for, you can see an example here: http://bl.ocks.org/mbostock/1009139
edit: just found a second example providing similar layout: http://bl.ocks.org/herrstucki/5684816
Here is a masonry layout for d3:
https://github.com/shawnbot/masonic
The demo:
http://shawnbot.github.io/masonic

Interactive Heatmap / Matrix Visualization

I would like to display on a webpage a heatmap (matrix) that I generate in R.
The matrix I have looks like this, but in my case the size is 300x300.
Basically I am looking for an interactive clustering, which would look like this :
http://online.wsj.com/article/SB125993225142676615.html#articleTabs%3Dinteractive
http://mbostock.github.com/protovis/ex/matrix.html
I would like to be able to clic on a branch which would then highlight the selected group/text, and fade out the rest of the matrix.
I have had a look around and cannot find much. I don't even know what language I should use for this ? JSON, Flash, HTML5, javascript, google charts ?
Any comments and advices would be extremely appreciated here.
Thanks.
I think that InCHlib - Interactive Cluster Heatmap library could be the solution.
Available from http://openscreen.cz/software/inchlib.
Google Visualization provides this heatmap option:
http://informatics.systemsbiology.net/visualizations/heatmap/bioheatmap.html
There's also this project that adapted it for more advanced uses and actually includes mouse-overs and tool-tips, as well as line magnification:
http://code.google.com/p/visquick/
You may also want to take a look at jQuery Flot, but be warned that WSJ uses a super expensive company called Tableau for data visualization and you are unlikely to find that level of visualization eye candy in an open source or free to use package.
Unfortunately, I had the same requirement. To create a Clustergram (Heatmap + Dendrogram) for a hierarchical clustering results.
There is no direct solution for this. I used ProtovisGWT (Choosel) to create dendrogram and heatmap seperatley and later combnied them.
If you just want js library you can use just protovis or d3.js to achieve this.
I would recommend using JavaScript for this task. Save your heatmap as SVG in R
svg("mymap.svg")
heatmap(...)
dev.off()
And then embed it into an HTML document as object
<object id="test-svg" width="800" height="600"
type="image/svg+xml" data="test.svg"></object>
Now, you can use JavaScript or ECMAScript to do all kinds of manipulations. I recommend to read one of the various online tutorials on this topic. E.g., you could get started with this one: http://www.petercollingridge.co.uk/data-visualisation/using-javascript-control-svg
Treemap of D3.js solves this beautifully. See here
http://mbostock.github.io/d3/talk/20111018/treemap.html
You could try http://amp.pharm.mssm.edu/clustergrammer/ . It is not written in R, but you can make an interactive clustergram by uploading a matrix file in tab-separated format and you will be returned an interactive (reorderable, searchable, filterable, etc) and shareable web-based visualization
D3heatmap provides interactive heatmaps with dendrograms in R based on the heatmap and heatmap.2 interfaces. It includes single row and column selection but does not currently allow selection of dendrogram branches.

How can I get Nodes and Links after being edited on the DiagramEditor?

In flex, I use IBM ilog Elixir to display network topology graph.
I maintain an xml file which in turn populates nodes and links arraycollections for Diagram to display.
Now, through Diagram Editor I perform some modification on diagram and hit save. I want to get all the nodes and links on editor to modify xml file while saving.
How can I achieve it?
I got the solution from other forum.
diagram.Graph gives us whole graph currently held in underlying Diagram.
so, now you can access graph.nodes and graph.links to get edited values.

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