Line No	File name
1	EPSRC-Materials, Mechanical and Medical Engineering-Materials, Mechanical and Medical Engineering-linkage.csv
2	EPSRC-Materials, Mechanical and Medical Engineering-Materials, Mechanical and Medical Engineering-significant.csv
3	Research Perspectives
4	http://www.researchperspectives.org/?page_id=43&SEARCH=
5

Node file name=EPSRC-Materials, Mechanical and Medical Engineering-Materials, Mechanical and Medical Engineering-linkage.csv

Line No	col1	col2	col3
1	2	11	0.085498
2	23	29	0.096137
3	4	21	0.096765
4	52	53	0.097545
5	25	37	0.097979
6	20	28	0.098201
7	54	78	0.098767
8	26	102	0.099697
9	22	108	0.099994
10	68	94	0.10021
11	42	74	0.10108
12	55	56	0.10175
13	44	111	0.1018
14	96	98	0.10217
15	33	110	0.10227
16	9	35	0.10237
17	71	90	0.10305
18	46	105	0.10342
19	61	113	0.10354
20	5	17	0.10386
21	114	115	0.10414
22	6	8	0.10474
23	85	95	0.10498
24	59	112	0.10526
25	14	48	0.10545
26	118	125	0.10577
27	18	126	0.10611
28	65	81	0.10616
29	58	100	0.10738
30	109	120	0.10769
31	41	127	0.10813
32	119	128	0.10832
33	31	107	0.10839
34	106	130	0.10857
35	87	129	0.1086
36	88	124	0.10863
37	66	73	0.10875
38	116	131	0.10879
39	40	86	0.10896
40	45	136	0.10963
41	51	69	0.10964
42	15	141	0.10987
43	47	138	0.10993
44	140	142	0.11025
45	63	121	0.11042
46	83	144	0.11055
47	75	123	0.11056
48	39	134	0.11082
49	117	146	0.1109
50	70	76	0.11102
51	80	89	0.11112
52	103	148	0.11126
53	133	143	0.11152
54	27	152	0.1116
55	132	153	0.11239
56	36	154	0.11256
57	50	139	0.11273
58	72	155	0.11279
59	64	158	0.11298
60	92	145	0.11329
61	84	150	0.11377
62	62	147	0.11385
63	149	159	0.11405
64	32	160	0.11458
65	34	162	0.11465
66	77	165	0.11465
67	97	157	0.1151
68	49	167	0.11535
69	163	168	0.11542
70	60	99	0.11562
71	156	169	0.11586
72	135	164	0.11589
73	19	171	0.1161
74	91	173	0.11641
75	43	174	0.11674
76	93	161	0.11749
77	166	175	0.11795
78	13	177	0.11803
79	176	178	0.1181
80	38	179	0.11907
81	12	180	0.11921
82	170	181	0.11946
83	79	182	0.12014
84	10	183	0.12084
85	30	184	0.1211
86	104	185	0.12196
87	82	186	0.12234
88	67	187	0.12265
89	7	188	0.12285
90	24	189	0.12436
91	57	190	0.12563
92	151	172	0.12769
93	101	122	0.12793
94	191	192	0.12817
95	16	194	0.12852
96	137	195	0.13354
97	3	193	0.20662
98	196	197	0.26562
99	1	198	1

Leaf file name=EPSRC-Materials, Mechanical and Medical Engineering-Materials, Mechanical and Medical Engineering-significant.csv

Line No	col1	col2
1	development
2	models
3	research
4	systems
5	design
6	project
7	materials
8	applications
9	control
10	techniques
11	proposed
12	measurements
13	engineering
14	structure
15	surface
16	imaging
17	industry
18	process
19	high
20	methods
21	generation
22	based
23	provide
24	technology
25	study
26	work
27	improve
28	time
29	required
30	effects
31	mechanisms
32	devices
33	cells
34	flow
35	performance
36	problems
37	approach
38	computer
39	aim
40	energy
41	understanding
42	increase
43	operation
44	reduce
45	complex
46	results
47	investigate
48	including
49	components
50	efficient
51	make
52	data
53	information
54	range
55	low
56	cost
57	potential
58	power
59	specific
60	properties
61	important
62	prediction
63	detection
64	large
65	advanced
66	composite
67	activities
68	patient
69	combination
70	level
71	test
72	uk
73	temperature
74	lead
75	simulation
76	optimisation
77	dynamics
78	recent
79	scale
80	ultrasonic
81	areas
82	achieve
83	analysis
84	conditions
85	interaction
86	programme
87	frequency
88	limited
89	particles
90	due
91	applied
92	acoustic
93	form
94	disease
95	physical
96	optical
97	support
98	signal
99	field
100	multi

Groups data will be displayed here.

Here will appear output in response to formation of groups using the green dragable threshold bar and the "Apply threshold" button, or the "Set no.of groups" toolbar.

Dendrogrammer v 1.0.5

The Dendrogrammer was created as one component in the analysis of multivariate data. In particular it is intended to allow already pre-processed data to be

classified into groups and then either
used in further analysis, or
used in some form of presentation about the data.

Current Features

Dendrogram construction
File read
File read now includes a manifest file which cues a clustering data file (node data) and a leaf description data file (leaf data).
File read now is integrated in the application page. Hard coded data loads if no data files are found.
Window width optimisation
Group formation by adjustable threshold
Cluster click/tap reports into dialog
Group formation reports with dialog, reports into separate tab, that tab pulses to notify. The pulsing stops when the tab is clicked
The threshold is a dragable element on the graph
The threshold can be adjusted also using toolbar buttons
The desired number of groups can be entered and it will set the threshold to fit
Leaf labels on the vertical axis. These are interactively styled in response to events.
Dialogs now guaranteed to be under 75% of window ht, scrolling if needed and using a default or wider width as appropriate on PC platform. Scrolling dialogs are not deployed on tablet platform as these are not suitable for tablets.
The group banding (and groups) can be removed with the "Remove" button
Summary dendrogram: For use in dendrograms with a very large number of leaves. Effectively truncating the dendrogram up from 0 ht to a level at which the structure can be discerned and then the clusters interrogated, rather than having hundreds of leaves along the bottom.
The Descendant Nodes Dialog contains a search link. The URL for this is specified in the .dat file which loads the data. The search link passes the cluster's leaf terms to a search engine.

Documentation

The technologies deployed in the application include

JavaScript - The major part of the application is written in JavaScript
Raphael Javscript library (by Dmitry Baranovskiy) - Used to make the dendrogram graphic elements. Raphael is truly amazing.
(Indirectly) SVG and VML - Raphael uses SVG or VML to do the drawing. Raphael switches seemlessly depending on the browser
jQuery - For some of the cross browser Dynamic HTML
jQuery UI - For some of the user interface supporting the application
HTML5 - Although there is nothing especially HTML5 about it really.
PHP - the data files are loaded using PHP.

The Dendrogrammer was created

by David Allan Robb
for his MSc project at Heriot-Watt University
in summer 2011

Quick-start Guide

In a nutshell-

Drag the green bar (Threshold bar) to adjust the dissimilarity threshold for group formation. Then click the "Apply threshold" button to form groups.
"Remove" will get rid of the groups.
Or enter the desired no. of groups in the "no. of groups field" and click the "Apply no. of groups" button.
To create a summary dendrogram, drag the threshold, then click "Truncate".
"Restore" redraws the original dendrogram.
Another way to adjust the threshold is to enter a number in the "Threshold value field".

Help

Dendrogram tab - View and interact with the dendrogram made from the clustering data.

Click or tap a cluster (element on the graph). Then read about that cluster in the dialog that appears.
That dialog also contains a search link. The URL for this is specified in the .dat file which loads the data. The search link passes the cluster's leaf terms to a search engine. It should open in a browser pop-up window or browser tab.
Adjust the green threshold bar and click the button to form groups of leaves (data points)
See more detail about the groups you form under the "Groups" tab.
The threshold can be adjusted by click-and-drag on the green bar, or using the threshold toolbar buttons, or entering a number in the "Threshold value field".
If you are using a tablet computer then drag on the green bar with your finger. If you find you can't drag the bar accurately then use the toolbar buttons to move the threshold. You might find that after moving the threshold bar away from the max with a button then you can get a better feel for how it drags using your finger.
If using the toolbar fine adjust buttons (plus and minus), note that the amount of movement with minus is set slightly less that with plus. This allows even more fine adjustment if you alternate from plus to minus around the point you are looking for.
To specify a given number of groups, enter the desired number in the field next to the "Apply no.of groups" button and click the button. The threshold will be chosen automatically for you.
To view a summary dendrogram (or truncated dendrogram), drag the threshold to some point below which you wish to discard the leaf detail. Then click the "Truncate" button. The resulting summary dendrogram will have everything below the threshold removed and be reshaped to fit the previous space. The origin is at the dissimilarity ht. you chose with the threshold bar. Tapping/clicking a cluster will still report all the leaf detail as before, despite the leaves being invisible. Groups can be formed in the same manner as before.
The "Restore" button will restore the original full dendrogram and the leaves as it was when you first viewed the current data. Loading new data or the same data again will have the same effect, as will reloading the page with your browser.
Use Control and + or - to zoom in and out ( or pinch on a tablet ). Look in your browser's View menu for more zoom controls.
What equipment to use: The dendrogrammer was designed to be cross platform (works on PCs with mouse and tablets with tap)
What browser to use: The dendrogrammer was designed to be cross browser. It is written in JavaScript (with a little bit of PHP to load the data). So it works in pretty much any browser that has Javascript enabled. However it is my experience that if one considers the latest browsers, the JavaScript interpreters in Firefox (Gekko with Tracemonkey), Safari (Webkit with Squirrelfish), and Chrome (Webkit with V8) are significantly faster (e.g. by a factor of 2 and more) than the "JScript" engine in Internet Explorer 8 and below (However, IE9 32-bit is good, but IE9 64-bit is reputed to be slow). So if one is seeking faster smoother performance with this particular application then one might wish to use Firefox, Chrome, or Safari (as at July 2011).

Data tab - Load different data or find out about the current data used to make the dendrogram.

A table of links is shown representing all the available data sets. Clicking a link loads that data set and makes a dendrogram from it.
The currently loaded data set is described and displayed in 3 tables
One table shows the contents of the .dat (or manifest) file. This contains meta data about the data set: the names of the two data files and a description of the data set.
The next table shows the contents of the clustering data file (or node file). This should be a csv file generated by MATLAB. It should have 3 columns. The first two columns are cluster or leaf designation numbers. The third column contains the merge height or similarity measure for that cluster.
The last table shows the contents of the leaf description data file (or leaf file). This is a csv file. The first row describes leaf number one. The second row describes leaf number two and so on. It should contain two columns. Column one should hold the short leaf descriptions or labels. Column 2 should contain a longer description for each leaf (this can be a repeat of the short label).
Loading a new data set or the same data set again will result in a page refresh and will clear any displayed groups or summary dendrogram which you may be displayed on the Dendrogram tab.
Adding further data sets can only be done by someone with write-access to the web space where the application resides (See 'Documentation' in the About tab.)

Groups tab- View the detail of the groups formed using the threshold adjuster and toolbar.

The detail can be copied and pasted into other software for further analysis or presentation.

About tab - Read about the application.

Help tab - This page you are reading now is the Help.

Zoom Help

If you find the leaf labels too small you may wish to zoom in. If you find your screen height too small to fit a large dendrogram you may wish to zoom out.

How to zoom on a PC or laptop

On most browsers Control and + will zoom in.
Control and - will zoom out.
Control and mouse wheel works too on most browsers.
Look in your browser's View menu for more zoom commands. E.g. Some browsers offer a separate zoom for text only. If using that, bear in mind that your browser sees the entire dendrogram including leaf labels as graphics.
Once you have zoomed, refreshing the page will adjust the dendrogram to fit the width you have chosen.

On a tablet device

Use the open or close pinch gesture to zoom.
Once you have zoomed in, as you would expect, refreshing the page does not affect the dendrogram size. It remains zoomed until you zoom back.

Summary Dendrogram feature

By setting the threshold bar and clicking "Truncate" you can reduce the amount of leaf detail displayed and reduce the height of the dendrogram.
Clicking a cluster on a summary dendrogram still reveals all of its descendant leaf detail in the dialogs. Group formation works as normal.
The "Restore" button restores the normal dendrogram.