JustClust User Manual
Contents
1. 3 Basic Usage of JustClust There are four main stages in using JustClust e Creating a network from data in a file on your computer e Clustering a network e Applying a layout to the network e Saving and loading the current session so that the above stages do not have to be repeated The following sections will describe these in detail 3 1 Creating a Network 1 To create a network while in the program go to File gt New Network from File 2 A box will appear with fields which you must fill in order to read data into JustClust New Network from File input File File Type Create Network 3 Click on the button with the folder icon and select the file on your computer which you would like JustClust to read 4 The File Type drop down box will be populated with file types 5 Choose one of the file types in the File Type drop down box 6 Click on the Create Network button 3 2 Clustering a Network 1 To cluster a network while in the program go to Cluster Analysis gt Cluster Network 2 A box will appear with a field which you must fill in order to cluster the network Cluster Network Clustering Algorithm Cluster Network 3 Choose one of the clustering algorithms in the Clustermg Algorithm drop down box 4 Click on the Cluster Network button The above steps will create a new tab in JustClust which will contain the clustering 3 3 Applying a Layout 1 To change the layo2. 5 JustClust JustClust User Manual Contents 1 Installne JustC lust 2 Running JustC lust 3 Basic Usage of JustClust 3 1 Creating a Network 3 2 Clustering a Network 3 3 Applying a Layout 3 4 Saving and Loading a Session 4 Exporting Data 4 1 Exporting a Network 4 2 Exporting a Clustering 4 3 Exporting a Graph Image 5 Toolbar Buttons 5 1 The Network Details Button 5 2 The Network Nodes Button 5 3 The Network Edges Button 5 4 The Network Clusters Button 5 5 The Search Network Button 5 6 The Filter Clusters Button 5 7 The Over representation Analysis Button 5 8 The Heat Map Button 5 9 The Microarray Heat Map Button 5 10 The Dendrogram Button 5 11 The Manage Plug ins Button 1 Installing JustClust To install and run JustClust you need Java which you can download here 1 Download the installer for JustClust 2 Open your computer s command line interface 3 Browse to the directory which contains the installer 4 Run the installer with java jar JustClustInstaller jar 5 Follow the instructions in the installation wizard 2 Running JustClust JustClust should be accessible from your desktop and or your application menu The following steps describe another way to start JustClust 1 Open your computer s command line interface 2 Browse to the directory which contains the JustClust jar file which was created during installation 3 Run JustClust with java jar JustClust jar
3. Session button 4 Exporting Data With JustClust you can export details about a network or clustering into a simple text file so that they can be examined outside of JustClust and in an easy to read format It is also possible to export a graph image into a high resolution image file which is suitable for use ina presentation or publication 4 1 Exporting a Network 1 To export a network into a text file while in the program go to File gt Export gt Network as Text File 2 A box will appear with a field which you must fill in order to export the network Export Network File Name Export Network 3 Click on the button with the folder icon and select the file on your computer which you would like to save into 4 Click on the Export Network button 4 2 Exporting a Clustering 1 To export a clustering into a text file while in the program go to File gt Export gt Clustering as Text File 2 A box will appear with a field which you must fill in order to export the clustering Export Clustering File Name Export Clustering 3 Click on the button with the folder icon and select the file on your computer which you would like to save into 4 Click on the Export Clustering button 4 3 Exporting a Graph Image 1 To export a graph mage into an image file while in the program go to File gt Export gt Graph as Image File 2 A box will appear with a field which you must f
4. e lated lel It ob Io ee IIS I ts RE BEP RE OU OF OE SIR EHT Tr m n Mm cae j Sa PSS eeenasssearalt tea SSeS 8 aaa eS eSn2952 85 Poo oGoe ee mognaeaagagc Pe PS PE PE BE PE BS PE PS BE RE BE PE BS BE RE BE RE BE eS qrttaertcrrtretrtrrtrtretrcrec se AFF X Trpn 5 at AFFX Or M10961 1_at AFFX Dr J01636 1_ at AFFx DOr pAsRed at AFFX Dr US 7609 2 at AFFX Dr J0134 4_ at AFF r2 Ee bioB M_ at AFFX r2 Ec bioB 5_ at AFF r2 Ee bioD 3_ at AFFX BioB M_at AFFX Dr AJ132968 1_ at AFFX Dr J01347 1_s at AFFSX Dr AF 298 69 1_ at AFFX DOr M10961 4_at AFFX r2 Ee bioC 5_ at AFFX Dr k01486 1_ at AFFxM Dr pOsRedi 1_s_at AFFX Dr J01636 4 at AFFX Or NM_131175 1_s_at AFFX Dr pd2EGFP_at AFFX Or GAPDH M_at AFFX Dr AJOO2662 1 s at AFFX LYS 5 at AFFX Dr x58 91 1_s_ at AFFX Dr US5943 1_ at AFFX Lys M_ at AFFX Dr GAPDH 3_at AFFX Dr ECOLOXB_at AFF X Thes M_at AFFX BioC 3_ at AFFX BioDn 3_at AFF X r2 Bs lys M_ at AFFX Dr S69414 1_s at AFFX Dr ABOY6373 1_at AFF X r2 Bs phe f_ at AFF X r2 P1 cre 5 at ee 5 9 The Microarray Heat Map Button The microarray heat map dialog is only available for microarray data and displays a heat map of the microarray values for the current network or clustering You can reduce the size of the microarray heat map by unchecking the Include Labels check box You can see the microarray value of a node in the Microarray Value text field by hovering the cursor over the corresponding square in the micr
5. e on your computer which you would like to use 2 Click on the button with the folder icon by the Gene Ontology Annotations text field and select the gene ontology annotations file on your computer which you would like to use 3 Select the row in the Cluster to Analyse table which contains the cluster you would like to analyse 4 Click on the Analyse Over representation button The over represented functions will be displayed in the Functions for Cluster table eB Over representation Analysis Gene Ontology pF Gene Ontology Annotations Oooo O Evidence Codes Lise Annotations EXP Significance Value 0 05 Multiple Hypothesis Testing Correction No correction 7 Cluster to Analyse Label Node 1 Mode 2 Mode 3 AFF amp Trpns 5 at AFFX Or M1096 AFFX Dr JO163 A SOA FX r2 Ec bio AFFX r2 Ec bio AFFX r2 Ec bio AFFX AFP X Dr AJ132 AFFX Dr JO134 AFFX DrAF298 4 Analyse Over representation Functions for Cluster Function 5 8 The Heat Map Button The heat map dialog displays a heat map for the current network or clustering You can reduce the size of the heat map by unchecking the Include Labels check box You can see the weight of an edge between two nodes in the Edge Weight text field by hovering the cursor over the corresponding square in the heat map Heat Map Include Labels Edge Weight a La k w tt ge Ran nan woth Ip oo
6. formation about the biological entity which the node represents E gt Network Nodes o x Label Visible Colour search Database All ee a enoc NN unto a eesosa e E Gnkto E O E O Tie AFPeDrAF202550 4 s at W B Tirk io AFFX Dr AF292560 1_s_at v B Link to 18 AFFX D AF298789 1_at W B Link to fw AFFX Dr AF323980 1_at p Link to T Mio O O inte Mino MEE Gn Min bint O Mino MEE tno t 22 AFFX Dr AJ132968 1_ at 23 AFFA DrAYOS6050 1_at AFFX Dr AY34234 _s at bed i 29 AFFX Dr ECOLOXB_ at 26 AFFX Dr ECOLOXL_at 27 AFFX Or GAPDOH 3_at 26 JAFFX Or GAPDH 5_at za 30 31 AFFX Dr J01347 2_at E Link to F 32 AFFX Dr J01347 3_at wl E Link to x D E a A 5 3 The Network Edges Button The network edges dialog allows you to alter the label visibility and colour of each edge in the current network or clustering For each edge which nodes the edge connects are displayed along with the weight of the edge B Network Edges xo i i Label Visible Colour Node 1 Made 2 A a o a E Oe O5 l A AFFx Dr Gapo AFFX Dr AJ002 1 6 f e AFFX Dr actat AFFX Dr actat 3 i BAF c0rpeteo aFPcDr Aso02 ie N 7 _ EM et i 2 i 23 M efi RAF Us 760 AFPXcDrwrO96 28 ft RAF ripnes_at FPO sora 2 RF nwt Jarre vores fi 23 i 30 A nr
7. ill in order to export the graph image Export Graph File Name Export Graph 3 Click on the button with the folder icon and select the file on your computer which you would like to save into 4 Click on the Export Graph button A graph image can be saved as a PNG JPG PDF or SVG file 5 Toolbar Buttons The toolbar to the left of JustClust s main graphical user interface contains 11 buttons Each button opens a new window which will allows you to observe and alter nformation about the current session 5 1 The Network Details Button The network details dialog shows you information about the current network or clustering B Network Details File homeflocallusernrJustClustdata microarray_data tab Fil parser Microarray file uses Pearson s productmoment correlation Ime taken to create network 83 milliseconds Modes 100 Edges T5 Average edges per node 0 75 smallest edge weight 1 8205250430093576 Largest edge weight 1 98902705742853113 Average edge weight 1 9133507 752896182 Clustering algorithm Complete linkage clustering algorithm ime taken to create clustering 368 milliseconds Clusters AO Wwerage nodes per cluster 2 0 Average edges per cluster 1 5 5 2 The Network Nodes Button The network nodes dialog allows you to alter the label visibility and colour of each node in the current network or clustering There are also links for each node to online databases with in
8. oarray heat map B Heat Map Include Labels Microarray Value a oo w ie m F EF cS a oy oy oH a cS a om oy m oo oo oo m m ho ho M M M i EF F EF EF EF F uf Cf uf TE g uf a co a 5 a a AFF M Trpons 5 at AFFX DOr M10S61 1_ at AFFX Dr J01636 1_ at AFF X Or pAsRed at AFFs Or US5 7609 2 5 at AFF X Dr J01 347 4 _ at AFF amp r2 Ee bioB fM_ at AFF amp r2 Ec bioB 5_ at AFF X r2 Ec bioD 3_ at AFF BioB M_at AFF Dr AJ132968 1_at AFF Dr J01347 1_5s_at AFF Dr AF298789 1_at AFFX Dr M10961 4_at AFF amp r2 Ec bioC 5_ at AFF Or K01486 1_ at AFFX Dr pOsRed1 1_s at AFFX Dr JO1636 4 at AFF Dr NM_131175 1_s_at AFF Dr pd2EGFP_at AFFX Dr GAPDOH M_at AFFX Dr AJO02662 1 5 at AFF X LyYSx 5 at AFFX Dr M56 91 1_s at AFF X Dr U54943 1_ at AFF Lys X M_at AFF Dr GAPDH 3_a t AFF Dr ECOLOXB_at AFF Thr M_at AFFX BioC 3_ at AFF BioDn 3_ at AFF X r2 Bs lys M_ at AFFX Dr S69414 1_s aft AFF X Dr ABO 6373 1_at AFF X r2 Bs phe M_ at AFF X r2 P1 cre 5 at AFF X Crex 3_ at AFF X r2 Bs thr 3_ sat AFFM r2 Bs thr 5 5 _ at AFFX Dr AF323980 1_ at AFF X r2 Ec bioC 3_ at AFFM Or M5 289 1_ 5 at Se 5 10 The Dendrogram Button The dendrogram dialog is only available for clustermgs which have been created by a hierarchical clustermg algorithm It displays a dendrogram for the current clustering Dendrogram 1 989 1 7901 1 5912 1 3923 1 1934 0 9945 AFF X r2 TagB_at AFF X D
9. r x03453 1_ at AFFX Dr U43284 1_ 5 at AFFS Dr AvYs34234 _ 5 at AFF amp Lys M_at AFFX Dr GAPDH 3_ at AFF Dr ECOLOXB_at AFF X Dr pd2EGFP_at AFF Or GAPDH M_at AFFS Dr AJOO2662 1 5 at AFF X DOr AYO56050 1_ at AFF X Dr AF292560 1 5 at AFFX Dr pOsRed1 1_ 5 at AFF S Or JO1636 4 at AFF M Or MM_131175 1_s_ at AFF S Dr J01 347 2 _ at AFFX Dr M1507 1_s_at AFF X Dr AF292559 2 at AFF X r2 Bs thr 3_ 5 _ at AFF M r2 Bs thr 5 5 at AFFX Dr AFS323980 1_ at AFF M r2 Bs phe M_ at AFF X r2 P1 cre 5 at AFF S Crex 3 at AFF M r2 Bs dap M_at AFF X Trpns 3 at AFF X Dr AJO02662 2 5 at AFF X Phex M_ at AFF Dapx M_at AFF M Dapx 3_ at AFF S Grex 5 at AFF X r2 TagC_at AFFX Dr U46493 1_ 5 at AFFS Dr JO1636 2 s at AFF S Dr AF292559 1_ at AFF X r2 Bs phe 5_ at AFF X r2 P1 cre 3_ at AFF X Dr actal M_at AFF X Dr actal 5 x _ at AFFM Dr actal 5_ at AFF X r2 Bs lys 3 at AFF S Or J01347 3_ at AFF X r2 Ec bioD 5_ at AFF X r2 Bs dap 3_ at AFFX BioDn 5_at AFF amp r2 Eec bioB M_ at AFF amp r2 Ec bioB 5_ at AFF amp r2 Ec bioD 3_ at A D e 5 11 The Manage Plug ins Button 1 To load file parsing plug ins into JustClust click on the File Parsers tab 2 Click on the button with the folder icon by the Parsing Plug ins Path text field and select the folder on your computer which contains the file parsing plug ins you want to load 3 Click on the Load Parsing Plug ins button The file types which can be pa
10. rsed by the file parsing plug ins you have loaded will be displayed in the File Types for Loaded Parsing Plug ins combo box 1 To load clustering algorithm plug ins into JustClust click on the Clustermg Algorithms tab 2 Click on the button with the folder icon by the Clustering Plug ins Path text field and select the folder on your computer which contains the clustering algorithm plug ins you want to load 3 Click on the Load Clustering Plug ins button The clustering algorithm plug ins you have loaded will be displayed in the Loaded Clustering Plug ins combo box 1 To load visualisation layout plug ins into JustClust click on the Visualisation Layouts tab 2 Click on the button with the folder icon by the Visualisation Plug ins Path text field and select the folder on your computer which contains the visualisation layout plug ins you want to load 3 Click on the Load Visualisation Plug ins button The visualisation layout plug ins you have loaded will be displayed in the Loaded Visualisation Plug ins combo box Manage Plug ins File Parsers Clustering Algorithms Visualisation Layouts Parsing Plug ins Path fhoamelocaluserJustC lust plugins parsing Load Parsing Plug ins File Types for Loaded Parsing Plug ins Microarray file uses Pearson s productmoment correlation
11. s at AFFX Dr U8996 1 3a fo f e AFFX Dr S6941 AFFX Dr ABO76 FFX Dr ECQL Iiii 1 E Lis II 1 A JAF F Dr pasre AFFX Dr U5760 1 Aa i a JAF FX Dr yo134 AFFX Dr AF 298 1 10 a JAF Fx Dr x5879 AFFX Dr U5594 1 413 A JAF Fx Lysx 5_at AFFX Dr U5594 1 te Feo sat arc O MnO96 _ 8 RAD apicw_at FPXCDapea_at 22 e JAFFx Dr pAsRe AFFX Dr M1 096 25 A RAFF x Dr pAsre AFFX Dr J01 34 ao a AF PcOrMs728 _jAFFx lt Or GAPD i Sst EM af a oA aa C O O a R ne ee ee 4 5 4 The Network Clusters Button The network clusters dialog allows you to alter the label node visibility edge visibility node colour and edge colour of each cluster in the current clustering For each cluster the amount of nodes it contains 1s displayed along with which nodes it contains B Network Clusters o x ks Label Nodes Visible Edges Visible Nodes Colour All S ld A A v v o bw o 3 n n E o O a a 5 CT n n 6 O n A T Ua n B n o S n n SS pio CT Ba e E v Bn a 2 BE o T T B3 ea a o S a a o n n e Bn o CU n n 8 S Ba a S oo n n E o S E a a n n S a n o B af n a a S a a s n a S S a a a n n B S n o lee B n n o ea a a B a a n o aJ n n aa ooo S o d A ah 5 5 The Search Network But
12. ton 1 To search the current network or clustering for a node edge or cluster enter part or all of the label of the item into the Search text field 2 Click on the Search button All nodes edges and clusters whose labels contain the search term will be displayed All edges connected to a node whose label contains the search term will be displayed All clusters containing a node whose label contains the search term will be displayed E Search Network xo search Nodes Label Node Options Edges Edge Options Clusters Label Cluster Options 5 6 The Filter Clusters Button The filter clusters dialog allows you to quickly make certain clusters in the current clustering invisible This may be useful if you want to focus only on clusters with a certain size or density 1 To filter the current clustering enter the relevant amounts into the various text fields 2 Click on the Filter Clusters button Filter Clusters show Largest Clusters a0 Hide Smallest Clusters eooo O Hide Clusters Above Node Amount CO Hide Clusters Below Node Amount Hide Clusters Below Density Threshold eooo Filter Clusters 5 7 The Over representation Analysis Button 1 To obtain probable functions for a cluster in the current clustering click on the button with the folder icon by the Gene Ontology text field and select the gene ontology fil
13. ut of a network while in the program go to Visualisation gt Apply Layout 2 A box will appear with a field which you must fill in order to apply a layout to the network Layout Network Visualisation Layout Apply Layout 3 Choose one of the visualisation layouts in the Visualisation Layout drop down box 4 Click on the Apply Layout button You can also manually change the layout of a network by left clicking on nodes and dragging them around Other controls for the network include zooming by holding down the right mouse button and moving the mouse vertically and panning with the keyboard arrow keys 3 4 Saving and Loading a Session Your current session in JustClust can be saved and loaded into from files on your computer 1 To save a session while in the program go to File gt Save gt Session 2 A box will appear with a field which you must fill in order to save the session Save Session File Name O i 3 Click on the button with the folder icon and enter the name of the file you would like to save into 4 Click on the Save Session button 1 To load a session while in the program go to File gt Load gt Session 2 A box will appear with a field which you must fill in order to load the session Load Session File Name i 3 Click on the button with the folder icon and select the file on your computer which you would like JustClust to read 4 Click on the Load
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