iTagPlot User Manual
Contents
1. MidExp 7 NTC NTC Pa HighExp 9 DNMT1 _DNMTL iz MAX TET2 _TET2 a DNMT3B _DNMT3B Mm TET1 _TETL Mm OK _Cancel Figure 4 5 Quantity group dialog Users can change criteria for grouping and choose sample names 4 2 3 K Means To group cluster features based on tag density navigate to the top menu bar and select Group gt K Means Figure 4 3 1TagPlot will show a dialog for options Figure 4 6 apply the k means algorithm to cluster features and samples based on tag density The result of clustering can be saved and opened with menu Save and Open figure Set clustering parameters Number of clusters 5 Distance metric Euclidean A Samples in a row Y Prefix cluster OK Cancel Figure 4 6 Cluster option dialog 4 2 4 ID conversion Enter delimeters and starting and end indices iTagPlot has a great function to map IDs in group files to those in sample files because annotation Feature in Sample GSTP1 NM_000852 1461 for groups could use different ID convention As PANA AEC Te shown in Figure 4 7 users specify a delimiter and ERAN E starting and end indices GSTP1 NM_000852 1461 is converted to Delimeters NM_000582 with delimiter of and starting As and end indices of 1 and 1 If IDs in samples and Eid ida l groups are the same users click button cancer Ok Cancel Figure 4 7 ID convention dialog 4 2 5 Delete group To delete groups choose or check groups and navigate to the to2. dpkg 1 1TagPlot 0 9 deb as non root dpkg deb x 1TagPlot 0 9 deb HOME The command for root and non root installs to opt 1TagPlot and SHOME opt ATagPlot respectively To run 1t double click the desktop icon or start menu or use the command line For a ZIP file unzip 1TagPlot 0 9 JDK 1 7 0 51 zip d out dir To run it run the following command out dir iTagPlot 0 9 JDK 1 7 0 51 41 TagPlot sh 2 DATA FILE FORMAT iTagPlot accepts data as a BAM or BED file for mapped reads and BED files for annotation to compute tag density of a sample The computation module generates a file for tag density The visualization module accepts a group file or quantity file 2 1 SEQUENCE MAPPING FILE Most mapping programs can generate a BAM file after mapping reads to reference sequences http samtools sourceforge net SAM1 pdf A BED file is a tab delimitated file and can store two different types of data In Table 2 1 the first row represents a mapped read and the second represents the score of a region While 1TagPlot counts the number of mapped reads for the former it uses the 5 column to average the score for the latter Table 2 1 Example of BED formats D A O E SL 2 2 ANNOTATION FILE An annotation file can be downloaded from online database servers e g the UCSC genome browser into various BED format because genomic features have different attributes In Table 2 2 the rows represent the annotation of RefSeq genes CpG isla
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4. for axes font in the Font family and Size comboboxes Font family lists all fonts found in your system and sizes a preconfigured to range between 6 57 pixels 5 2 5 Changing X and Y axis Preferences gt X Axis and Y Axis allow customizing grid lines tick marks and labels visibility tick interval and max count and tick width and length for the X and Y axis Preferences gt X Axis and Y Axis has additional options for data transformation and smoothing 5 2 6 Changing scale and range Preferences gt Scale allows customizing the axis Preferences scale The scale can be changed individually for each axis The scale range 1s 1 2 5 and defaults to 1 Reset axis scales resets the scale to 1 for X and Y axis As shown in Figure 5 7 users can use axis scale sliders in the view panel by hovering over the horizontal x axis and vertical y axis sliders clicking 8U gt Axis scale sliders left and Y axis range slider on the control ball and dragging mouse left or right right and up or down respectively to change the value The right plot of Figure 5 7 shows a double slider to set the range of the Y axis 6 GRAPHING TOOLS 1TagPlot provides multiple tools for further edit the appearance of a generated graph To use these tools user must first upload D pr T sample data and generate a graph The tools are located in the Move m l a control bar on top of the user interface as show in Fi
5. 1T agPlot User Manual iTagPlot is a tool to accurately compute and interactively visualize tag density read coverage from genomic sequencing data The software includes a computing module highly interactive user interface and graphing tools with many options for creating tag density and customizing the graph 1TagPlot computes and draws the average tag density of all or groups of features for each sample In addition iTagPlot computes and visualizes the tag density of individual features of interest and groups of features based on quantitative values such as gene expression DNA methylation CpG density and even quantiles of quantitative values The software supports parallel computation using a grid engine and customize drawing properties easily in a user friendly interface Given that tag density plots are a mainstay of manuscripts describing epigenomics data based on next gen sequencing it 1s essential for biologists to have access to software that can generate these plots easily E AA ca 3 Dilo RESTE QUISE SA EA AA ee 3 122 Inmstallimo and usma FLAG Po a tias 4 Ps A e 4 OS A ees 4 AS LAO UNIA o 4 2 DAST O Ona an nd E see ah toeaceute teen nenanees 4 Za Deden IVI AD WIN le nd babe uate adi detawnce ed bao E 4 22 AMOO PACs i cite adi tea ad Au eae eiiiad ie aetualeb etl Winnie luted hte c tins 5 2 3 Annotation configuration file cccccccccccccsscceeesssssssseseeeeeeecccceeeeesasaeeeeessssseseeeeseeeeeeees 5 e Nek STASI YING at
6. 8902 TNFRSF18 45 NM_080605 B3GALT6 43 NM_016176 SDF4 44 NM_016547 SDF4 46 NM_001014980 FAM132A A a a a a E 2 6 QUANTITY FILE Quantity file includes list of feature names along with quantitative values such as expression and methylation for samples Table 2 6 shows an example of quantity file structure The purpose of the quantity file is to allow easy creation of subsets groups of features based on quantitative values and calculating the average of the subset data Therefore user should upload sample files before quantity files Table 2 6 Example of quantity file A a i ee ee el 3 gt COMPUTATION OF TAG DENSITY To compute tag density of enrichment data mapped reads users specify input files in the BAM or BED format an annotation configuration file an output directory and choose Enrichment for Data Type An annotation base directory should be specified if a configuration file is in the different directory of annotation files 1TagPlot supports several running modes to use a single and multiple cores and grid engine Users should specify the command for a grid engine 3 1 ENRICHMENT DATA Figure 3 1 shows an example to compute tag density for 6 ChIP seq datasets using a grid engine with 4 jobs Note that the input files have mapped reads and the fragment size should be specified to lengthen reads to the original size Samples Browse r data toydata sequencing bam DNAme bam data toydata sequencing bam DNMT1 bam t d
7. F 0 150 refseq intergenic a as 0 100 refseq promoter body d refseq body 0 050 refseq downstream 0 000 refseq promoter body 4000 3000 2000 1000 0 25 50 75 20 1020 2020 3020 4000 refseq body downstream lt Je Figure 5 2 Generated graph Sample name KA DNAme Y 0 00 D la H3K36me 3 m H3K4me3 DNAme CpG 86 17969 la H3K9me 3 DNAme CpG 36 10026 H3K27me 3 i DNAme ch f res lt A a 4000 3200 2400 1600 800 0 20 40 60 80 100 800 1600 2400 3200 4000 o iI Feature name Figure 5 3 Generated heatmap Note that chosen features and groups will be enumerated for each chosen sample and the checkbox T will not draw the date items as shown in Figure 5 4 NPIeS amp groups Computation Sample Group Export View a PO ATP IE Har Oa i H3K9me 3 a H3K27me3 i E DNAme HCP E DNAme HighExp Mi DNAme ICP MM DNAme LCP E DNAme LowExp W DNAme MidExp A DNMT1 E DNAme coding Ml DNAme noncoding DNMT1 HCP E DNMTI HighExp W DNMTL ICP E DNMT1 LCP E DNMTI LowExp W DNMT1 MidExp W DNMTL coding E DNMT1L noncoding l DNMT3B aces eature name 0 225 FMOS NM_001461 2152 WDR44 NM_001184966 0 200 EIFIAD NM_0012424811 SATB1 NM_001131010 6 0 175 RRP7A NM_015703 39146 HARBI1 NM_173811 2302f C14orf132 NM_0012525 0 125 SAIS 0 100 0 075 VA EA 0 050 RA MidExp KA ICP 0 025 KA HighEx
8. MT3B H3K27me3 H3K36me3 H3K9me3 M HighExp Y LowExp a jw E LD z L Figure 5 6 Heatmap with samples in a row 5 2 3 Changing colors Preferences gt Colors allows customizing graph and heatmap colors Users can change the following options drawing area graph background graph area plot background graph border graph title color axes labels color legend labels legend background x axis gridlines y axis gridlines tick labels along axes tick lines along axes symbol fill These values can be set to any color in the RGB range For heatmap users can choose preset color scheme or change colors for gradient iTagPlot also allows changing data series colors To change a plot color hover over the specific series line or area which will change the mouse cursor to a hand Then right click on the mouse and a context menu will appear For line graph there is an option to change the line color For an area graph there is an option to change the line color and area fill color Changing the current selection will change the series color respectively 5 2 4 Editing text and fonts Preferences gt Labels allows setting and changing graph title and axes labels These are all optional and can also be left blank It also allows customizing axes fonts The axes fonts are controlled by the same variable and therefore cannot be set to different values for each axis If or once the object is set to Axes you will see the current settings
9. ata toydata sequencing bam DNMT3B bam data toydata sequencing bam H3K4me3 bam r data toydata sequencing bam H3K9me3 bam data toydata sequencing bam H3K27me3 bam data toydata sequencing bam H3K36me3 bam Compute Annotation Configuration File Browse Users jechoi research tagviz data toydata sequencing annot Annotation Base Directory Browse Output Directory Browse fUsers jechoi research tagviz data toydata sequencing test Running Mode Serial Multi core Grid engine Grid command Threads 4 qsub cwd V j y b y sync y N itagplot Data Type Enrichment Fragment size 300 Beta score Column number File type pang ly Cancel Figure 3 1 Tag density computation for 7 sequencing datasets in the BAM format using a grid engine with 4 jobs 3 2 SCORE DATA Figure 3 2 shows an example to compute tag density for score based data The column number should be specified for the score Samples Browse Annotation Configuration File Browse Users jechoi research tagviz data toydata infini um annotatic gviz data toydata infinium bed DNMT1 cg bed Annotation Base Directory Browse gviz data toydata infinium bed DNMT3B cg bed gviz data toydata infinium bed NTC cg bed Output Directory Browse gviz data toydata infinium bed TET1 cg bed Users jechoi research tagviz data toydata infinium test gviz data toydata infinium bed TET2 cg bed Running Mode gviz data t
10. ees a Uw de bao ent a T O al O A A OO Sul DAVIN PECTIC CES rada dai oe S2 EAS IS E de SL POW Sd IS idos S22 SA a acaaustaccaesescaioss Sl de data Panel ONY todabia ido ais SN EOS dada 1 GETTING STARTED 1 1 PREREQUISITES To use 1TagPlot you will need the following programs e perl 5 8 5 or later e samtools 0 1 6 or later e perl modules in most perl distribution as default Getopt Long File Basename File Which File Spec Cwd POSIX You need to add the directory of perl and samtools into your PATH 1 2 INSTALLING AND USING ITAGPLOT Y ou can download the release and data from https sourceforge net projects itagplot files release 1 2 1 Mac OS X For installation download iTagPlot 0 9 macosx dmg double click the file and drag and drop the icon into the Application folder To run it double click the desktop icon or start menu 1 2 2 MS Windows For installation download iTagPlot 0 9 windows7 msi and iTagPlot 0 9 windows8 msi and double click the file To run it double click the desktop icon or start menu 1 2 3 Linux or UNIX For installation download an appropriate version of iTagPlot 0 9 x86_64 deb iTagPlot 0 9 x86_64 rpm and iTagPlot 0 9 JDK 1 7 0_51 zip and run a following command as root or non root For a RPM file as root rpm 1vh 1TagPlot 0 9 rpm as non root rpm install badreloc relocate FSHOME dbpath SHOME rpm db nodeps noscripts TagPlot 0 9 rpm For a DEB file as root
11. gure 6 1 Joao Figure 6 1 Toolbox toolbar 6 1 MOVE TOOL Toolbox gt Move allows moving a graph once its size exceeds the size of the graphing area To enable the move tool click on the move button When move tool is enabled hovering over the graph will show a hand cursor 6 2 DRAW TOOL Toolbox gt Draw allows free hand drawing over the graph area To enable the draw tool click on the draw button When draw tool is enabled hovering over the graph will show an arrow cursor To begin drawing press down on the left mouse button and continue to keep it down as you drag along the graph area To stop drawing release the mouse button To delete a path right click the mouse over it 6 3 WRITE TOOL Toolbox gt Write allows adding custom texts over and around the graph area To enable the write tool click on the write button When write tool is enabled hovering over the graph will show a text cursor 7 EXPORTING GRAPHS 1TagPlot allows saving a generated graph as an image or as a PDF or EPS file The function will save an exact image of what is in the graph area excluding the scaling sliders and range double slider as shown in Figure 5 7 This means it includes any changes to axes scaling and application of Draw and Write tools 7 1 EXPORT AS PNG This feature will save an image of the generated graph To being export navigate to the top left menu bar and select Export gt Export as PNG Clicking o
12. its width 3 3 ERRORS 1TagPlot will generate error messages when invalid requests occur The error message appears in the top ee ee x right corner of the user interface The error message TEETE E includes a header and short description of the cause before using this too Error messages fade automatically after a few seconds or it can be hidden immediately by clicking 2ure3 1 Error message box on a X icon in the top right corner Figure 8 1 shows a sample error message
13. limited The first row describes the data headers and will be used to populate the graph axes All subsequent rows describe features and contain the plot data Table 2 4 displays a simplified example of sample file structure 1TagPlot data parser will interpret sample columns as follows Feature name Feature chromosome type string Start value type int 2 3 4 End value type int 5 Strand ignored 6 n Feature data type double Table 2 4 Example of tag density file Key Ref Start End Strand 5000 4980 4960 4940 CpG2400 chrl 1167000 1168985 1 844 1 800 1 862 1895 CpG2753 chrl 1173914 1174263 1929 12072 12156 2 211 Ess ss Lo os se Ss SS SS E SS SS SS Oe SS O a o 2 5 GROUP FILE Group file includes list of feature names separated by tab character Table 2 5 shows an example of group file structure The purpose of the group file 1s to allow easy creation of subsets of features and calculating the average of the subset data Therefore user should upload sample files before group files 1TagPlot parser will read the contents of the group file and look for matches in the names of existing features 1TagPlot will ignore group file if it does not match any existing features Table 2 5 Example of group file ARA 21 NM_152486 SAMDI11 22 NM_015658 NOC2L 23 NM_198317 KLHL17 28 NM_001142467 HES4 30 NM_198576 AGRN 32 NM_017891 Clorf159 39 NM_ 004195 TNFRSF18 41 NM_14
14. n the option will display a file chooser dialog that request a file name and file type File type is preset to PNG and there are no other options File name can be set freely After setting the filename click Save 1TagPlot will then generate a snapshot of the graph area and save it as PNG image in the specified location The dimensions of the generated image are relative to the actual size of the graph area 7 2 EXPORT AS PDF AND EPS This feature will save a PDF or EPS file of the generated graph To being export navigate to the top left menu bar and select Export gt Export as PDF or Export as EPS Clicking on the option will display a file chooser dialog that request a file name and file type File type is preset to PDF or EPS and there are no other options File name can be set freely After setting the filename click Save 1TagPlot will then generate a snapshot of the graph area and save it as a PDF file in the specified location The PDF or EPS document defaults to 1 page letter size If the graph width exceeds its heights the generated PDF or EPS will be landscape else it will be portrait If the graph is scaled and the size of the graph exceeds the size of 1 letter page the graph will scale down to fit the page size 7 3 SHOW EXPORT iTagPlot enables setting an option to launch a generated PNG PDF or EPS file upon export This option 1s located in the menu bar and can be change by navigating to Export gt Dis
15. nds and DNase clusters They have different number of columns Table 2 2 Example of annotation chr21 11020841 11098925 BAGE3 NM 182481 chr21 10895511 10895781 CpG 30 a chr21 15355105 15355308 FAIREOnly 70565 1000 l 15355105 15355308 2 3 ANNOTATION CONFIGURATION FILE For easy computation of tag density 1TagPlot uses an annotation configuration file Table 2 3 The first and second columns represent the name and file of each feature respectively The third represents column numbers that are used to build an identifier of features in a tag density file The fourth and fifth represent the number of bins in body and up down stream of features The sixth represents the length of up down stream The last specifies in which regions tag density is computed 5 for up stream and body 3 for body and down stream and 0 for all regions As shown in the last row reference sequences to be filtered can be specified Table 2 3 Example of annotation configuration file e IDCal BodyBin StreamBin SteamLength Type cgi hglOcpgisiandbed 4200 200 4000 0 A E ST refseq hgl9 efsegbed 145 500 1500 5000 O Cos hglOefsegbed 45 1500 500 5000 5 Cs bgl9xefieqbed 45500 500 S00O 3 er mM IS _ IS 2 4 TAG DENSITY FILE Tag density file uses newline character as a row separator and tab as a column separator There has to be the same number of columns for each row The number of rows 1s not
16. os samples features and groups comers pas 10746 CpG 140 To generate a plot navigate to the left of user interface and DE select samples and features and or groups you wish to OR visualize Select one or more items from by clicking on ee the checkbox next to its name Figure 5 1 illustrates ape nec selecting two features To deselect a data item click on the checkbox again until the checkmark disappears 7966 CpG 69 After selecting one or more items click on the Chart or 10168 CpG 21 Heatmap button in the top left corner A chart or heatmap will appear in the view panel as shown in Figure Figure 5 1 Selecting data items 5 2 or Figure 5 3 0090 e TagPlot 0 9b 7 samples 7 groups 27388 features Computation Sample Group Export View y d Ke E E a ak A ANRT Chart Heatmap Reload Graph Cluster Colors Labels X Axis Y Axis Scale Move Draw Write Generate yl Preferences Toolbox 1 Sample name Y DNAme F H3K36me3 E DNAme E DNAme CpG 36 10026 E DNAme CpG 86 17969 0 700 H3K4me 3 m H3K9me3 0 650 H3K27me3 0 600 Search features 0 550 mala Feature name a CpG 366 17612 0 500 CpG 366 20317 CpG 368 21729 0 450 CpG 369 17754 0 400 Y CpG 36 10026 CpG 36 10063 0 350 PA CpG 36 10141 0 300 CpG 36 1022 CpG 36 10221 0 250 0 200 ul Group name m refseq promoter
17. oydata infinium bed TET3 cg bed Serial 8 Multi core Grid engine Grid command Threads 4 Data Type uy Enrichment Fragment size Beta score Column number 5 File type BED z Compute Cancel Jsers jechoi research tagviz iTagPlot dist run418082548 bin tag_density o Users jechoi research tagviz data toy ading feature configuration from Users jechoi research tagviz data toydata infinium annotation hg19 conf inning jobs for Users jechoi research tagviz data toydata infinium bed DNMT1 cg bed idy 200 Stream 200 Length 4000 Missing NA Type bed IDCol 4 Score 4 Filter chrM ading Users jechoi research tagviz data toydata infinium annotation hg19 cpgisland bed ocessing Users jechoi research tagviz data toydata infinium bed DNMT1 cg bed wll done wl2 done wl13 done w14 done O i A _ Y D O Figure 3 2 Tag density computation of Infinium 450K array data in the BED format with 4 cores 4 LOADING DATA 4 1 SAMPLE Open Sample 2 Delete Checked Sample 4 1 1 Open sample To load samples navigate to the top menu bar and select Uncheck All Invert Check Sample gt Open Sample Figure 4 1 f xit A 1TagPlot will attempt to retrieve and parse the requested file A blue progress bar will appear in the interface to indicate load LU 41 Sample menu process is being handled After samples are successfully I Sample name read the samples and their features will a
18. p LowEx p 0 000 Y LCP 5000 4000 3000 2000 1000 0 20 40 60 80 10 1010 2010 3010 4010 5000 CA coding a Figure 5 4 Area graph for various groups without drawing features 5 2 MANIPULATING VISUALIZTION 1TagPlot allows customizing many aspects of the visualization using the toolbar as shown in Figure 5 5 et oe Figure 5 5 Preference toolbar 5 2 1 Editing graph Preferences gt Graph allows customizing several aspects of the graph graph type legend location and point mark line weight and maximum number of seriesEditing colors 5 2 2 Editing heatmap Preferences gt Cluster allows customizing several aspects of the heatmap clustering algorithm samples in a row distance metric linkage method the number of clusters for k means and the height of rows in pixel Computation Sample Group Export View 1 ne Ko ln aa DE Elle Q 3 e TO Chart a_i Reload Graph Cluster Colors Labels X Axis Y Axis Scale Move Draw __ __ Write Generate Preferences Toolbox Y Sample name iw H3K27me3 g o A Y DNMT1 noncoding Y DNMT3B gt Search features ICP CAN Feature name HCP Y WDR44 NM_001184966 coding Y EIFLAD NM_001242481 gt izd MidExp Group name HighExp Y LowExp Y HCP LCP Y MidExp Y 0 100 0 100 0 100 0 100 0 100 0 100 ICP DNAme DNMT1 DN
19. p menu bar and select Sample gt Delete Checked Group or Delete Selected Group The user interface will update and the selected groups will no longer be visible in the lists of groups 4 2 6 Change group name To change a group name click the group name in Figure 4 2 and then edit the name 4 2 7 Context menu To show a context menu click the right button of mouse It has several functions to check uncheck and select unselect groups 4 3 SEARCHING FEATURE iTagPlot enables searching through uploaded features using a search function To use this feature Y Search features navigate to the left of the interface and look for a bar with label Search features Clicking on the bar will toggle the visibility of the search field The search field is displayed in Figure 4 8 Feature name 10746 CpG 140 To search for specific features type a text into the search field and press ENTER iTagPlot will search 17735 CpG 86 for matches in feature whose name contains the 17869 CpG 36 substring entered into the search field l Figure 4 8 Search feature To clear the search results and redisplay the full list of features either delete the input from the search field and press ENTER or click on the Search features bar The latter will also hide the search field 5 VISUALIZATION 5 1 GENERATING A PLOT Generating a plot requires some data 1s first loaded into the system 1TagPlot allows plotting a selection of ene S
20. p name noncoding iTagPlot will show a dialog for ID conversion attempt to za retrieve and parse the requested file A blue progress bar ICP will appear in the interface to indicate load process 1s LCP being handled After a group is successfully read the coding group will appear in the user interface as shown in Figure _ 44 Figure 4 4 Goup table 4 2 2 Quantity group To load groups based on quantitative values navigate to the top menu bar and select Group gt Quantity Group gt Microarray RNA seq Beta Values or Quantile 1TagPlot will show dialogs for ID conversion attempt to retrieve and parse the requested file A blue progress bar will appear in the interface to indicate load process 1s File Content choose the type of columns E CCT Feat 7 ji Sam zi Sam zili Sam Z li Sam Z Sam Z Sam sali Gene DNMT1 DNMT3B NTC TET1 TET2 TET3 A1BG 5 6477 5 894865 5 72845 5 679005 5 656745 5 782065 A2LD1 5 11163 5 26496 5 37417 5 341455 5 25296 5 275185 A2M 6 84574 6 6877 8 436425 5 313045 5 066575 5 261665 A2ML1 8 81842 8 77396 7 73616 7 692365 7 96755 8 02887 AAAS 10 05333 9 94205 10 3161 10 2293 10 04735 10 05465 AACS 8 821745 8 95943 8 45979 8 454395 8 572955 8 36932 AAGAB 8 190345 8 14519 8 69726 8 106995 7 914725 8 0035 Criteria modify names and cutoffs Name Mapping choose sample name Name Cutoff Loaded Sam ple File Header LowExp MIN TET3 _TET3 A
21. play file If the checkbox is checked 1TagPlot will open an exported file automatically upon completion of the export function If the checkbox is not checked 1TagPlot will generate the file but not open it for preview OTHER FUNCTIONALITY 8 1 SAVING PREFERENCES 1TagPlot will automatically save preferences such as graph type colors fonts etc This functionality is enabled by default and will execute whenever preferences are changed The settings will be saved in the same file where the executable application 1s saved so it is advisable to save the application in a writable directory The preferences are saved in a file titled settings If this file is deleted or corrupted graph preferences are set to their defaults 8 2 SIDEPANELS VISIBILITY To enhance analyzing the graph it is possible to toggle the visibility of both data panels on the left and control bar on top of the user interface 8 2 1 Show sidepanels To hide both panels press CTRL 1 or use the top menu bar and navigate to View gt Collapse Sidepanels 8 2 2 Hide sidepanels To show both panels press CTRL 2 or use the top menu bar and navigate to View gt Show Sidepanels 8 2 3 Hide data panel only To adjust the size and or visibility of data panels only bovver over the vertical separator between the data panels and the graph area click and drag the mouse Dragging to the left will reduce the width or hide the panel and dragging to the right will increase
22. ppear in the user TE interface as shown in Figure 4 2 A id Y DNMTI 4 1 2 Delete sample vi Ter Y DNMT3B To delete samples choose or check samples and navigate w tm to the top menu bar and select Search features Sample gt Delete Checked Sample _ Feature name or Delete Selected Sample STRA13 NM_144998 112 ZNF419 NM_001098495 4 1 3 Change sample name MCF2LINM_024979 4923 i ARAP1 NM_001135190 1 To change a sample name click the sample name in INDC OAST OORT Figure 4 2 and then edit the name CSF3 NM_001178147 10 CX3CL1 NM_002996 8529 4 1 4 Context menu ANGEL1 NM_015305 5751 To show a context menu click the right button of mouse e soii It has several functions to check uncheck and Figure 4 2 Sample and feature tables select unselect samples 4 2 GROUP 1TagPlot supports various way to define a group of features 1 a group file list features that belong to the group 2 a quantity Open Group file has quantitative values such as gene expression DNA Quantity Group methylation and enrichment scores that use to define groups K Means based on criteria 3 k means clustering algorithm is applied to MSigDB determine groups based on tag density and 4 MSigDB is a database to define gene sets related to biological function and a T Check All pathway 4 2 1 Open group Invert Check To load a group navigate to the top menu bar and select Figure 4 4 Group meni Group gt Open Group Figure 4 3 I Grou
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