XYLab User Manual
Contents
1. axis margin Thanks to this one can easily adapt the program to fit a specific region of the screen In addition the ctrl f shortcut sends the plot to full screen mode for the highest visibility while a next press of ctrl f revert to the normal visualization Menu controls and options Data Copy Load select an input file to open from which to extract data Paste use data copied elsewhere as input Save current data produce a text file with current X Y and Label for all entities Save visible data produce a text file containing the whole multivariate dataset but only for visible entities Single paste in the copy paste area only the currently selected X Y and Label for the copied entities Full paste in the copy paste area the full multivariate data for the copied entities Highlight copied mark copied entities those in copy buffer in the plot Highlight while copying mark copied entities on the fly in the plot Remove highlights remove the entities marked by the two functions above not that introduced by find Save copy buffer save the content of the copy paste area Clear copy buffer clear the content of the copy paste area no undo X Axis Y Axis Labels Find Points Config Labels on off display hide the labels in the plot axes Full display the axis labels with maximal precision lab real Int display the axis labels as the integer of the value lab int real Sci display the l2. file in the copy paste area to be modified Save current conf write the current configuration in the X YLab conf file The configuration file XYLab conf At the time of the first startup XYLab places a configuration file in the user home folder eg home you in Linux or c Documents and Settings you in windows This conf file stores your visualization preferences i e the size of the polt area the proportion of that with axes and so on Each time you interact with this geometry manager with the arrow keys or with dedicated functions in the Config menu this file is updated This means that the next time you use the XYLab it will remember you last geometry configuration On the other hand once you feel comfortable with the interface and the plot area proportions the conf file should be left unchanged Here I ll explain briefly this conf file It contains something like this XYLab configuration file followed by several configuration parameters that I ll explain here briefly plot_width 800 plot area width plot_height 600 plot area height area_mov 10 pixels associated to the Altt arrows press see above x_ax_dist 10 of the plot area from x axis to the bottom margin y_ax_dist 10 of the plot area from y axis to the left margin axes_mov 1 associated to the control arrows press see above copywin_height 5 the initial height of the copy paste window in characters x_label_size 8 size of the labels for th
3. XYLab User Manual Matteo Ramazzotti matteo ramazzotti unifi it Introduction XYLab has been written for the analysis and the real time post labelling of multivariate data It is basically an XY plotter with the additional feature of pop up labels when the mouse rest over a plot point Everything in the dataset can be a label including the other plottable i e numerical columns and non plottable text labels e g annotations Although below average in terms of graphics XYLab offers unprecedented tools such as text in plot search with dedicated point highlighting system and select n paste which greatly helps in outliers characterization XYLab is free for non commercial use only In all other cases please contact the author Interface architecture The program has four main areas 1 menu with controllers for adjusting the other areas 2 plot area where the data point are displayed 3 paste area where the points are annotated 4 control area where the control tools are placed XYLab by matteo ramazzotti unifi it 2007 Data Copy Xaxis Yaxis Labels Find Points 0 8481 0 8002 0 7523 0 7044 0 6565 0 6086 0 5607 0 5128 0 4649 0 417 un T T I T T m t T ad 0 102 0 1754 0 2488 0 3222 0 3956 0 469 0 5424 0 6158 0 6892 0 7626 Z col cal min 0102 maxj 0 836 Log Norm Std Cent Value 0 y col focai min 0 417 max 0 896 Log Norm Std f Cent Value 0 Labe 1s Annotat
4. a values organized in a table with column headers as the first row The current XYLab distribution contains a sample input file Escherichia txt with the typical format It should be sufficiently self explanatory It contains 4240 rows x 18 columns 76320 data points Columns 11 13 15 16 are non plottable Their column headers should not appear in the X and Y controllers but only in the Label controller In addition XYLab recognizes GenePix gpr files and skip non data rows header loading only useful data Basic plotter usage At start up the program shows an empty plot area The data are loaded with the specific command from the menu Otherwise the data can be pasted directly from external applications such as text files MS Excel OO Calc etc The program read the input data table see below and auto detect the first two plottable columns e g the ones with numbers only and the first non plottable one e g the one containing non numerical values The plot then appears with X Y and Label controller set up to the detected columns the data are plotted as black circles Their shape size colour can be adjusted from the Points menu When the X or Y columns are changed from the axes controllers the plot updates accordingly wow If the mouse is left over a point for a little time you can control this delay time with the PgUp and PgDn keys a pop up labels appears containing the value corresponding to that point in the column selected from th
5. abels with scientific notation with three decimals Increase font increase the font size of the labels Decrese font decrease the font size of the labels Single pop up labels containing only the value selected in the Label controller affect also Find gt Save Full pop up labels containing the full multivariate dataset affect also Find gt Save Permanent on off labels are not popped up but always visible in the plot area Increase font increase label font used in permanent mode Decrease font decrease label font used in permanent mode Mark last copied used after a copy highlight the last copied entities Save save the found entities as text file Increase size increase the size of the highlighted entity Decrease size decrease the size of the highlighted entity Toggle empty filled change the display of the highlighted entity Toggle circle square change the shape of the highlighted entity Rotate red black blue green change the color change the shape of the highlighted entity Increase size increase the size of the entities Decrease size decrease the size of the entities Toggle empty filled change the display of the entities Toggle circle square change the shape of the entities Rotate red black blue green change the color change the shape of the entities Reload factory defaults restore the display values used the first time XYLab was launched Show current conf display the content of the XYLab conf
6. e Label controller Obviously the content of the label can be changed from this dedicated controller Changes in the X and Y min max entries adjust the regions of the plot to be displayed after the Enter key is pressed in the keyboard With the left mouse button pressed you can create a zooming rectangle in a defined are of the plot When the left button is released the plot will be zoomed in the selected area You can zoom in as much time as you want The right mouse button makes zoom out step by step The find function This function is pretty innovative for a plotter it allows to use the column specified in the Labels controller for keywords searching To use this function the find line must be filled with some keyword string When the Enter key is pressed the keyword is searched The search result is graphically displayed on the plot selected points will grow in size and change in color becoming easily identifiable in the plot area The Lock Unlock button is initially in the Unlock mode meaning that plotted entities will stay highlighted if you change the X and Y columns but likely will change if you change the Label column As an example if use the escherichia_dataset txt input file you ll have several points highlighted with the ribosomal keyword if the Label column is Annotation but if you change this column to COGClass no points will become highlighted simply because the COGClass column does not contain protein ann
7. e x axis y_label_size 8 size of the labels for the y axis ballon_label_size 5 size of the labels for the ballons that pop up on mouse rest label_delay 100 the delay time for the labels to pop up Availability XYLab is mainly distributed as a script code to be used in OSs with Perl 5 8 or above installed and equipped with the Tk graphical interface This is to maintain the highest portability I can provide a fully functional PAR compiled version to be used in Windows or Linux perl free environments Warning the XYLab is free for non commercial use only Caveats Due to a graphic misbehaviour during initialization when the XYLab is launched for the first time in linux its dimensions could appear exaggerate and the copy and control area below the bottom screen margin To solve this issue you ll have to load a dataset then refer to the paragraph Adjusting the visualization of this manual Basically you ll have to manually resize the program until it fits your screen This configuration will be saved for further usage so next time you start the XYLab everything should work fine Bug report Please report any bug or suggestions to me matteo ramazzotti unifi it Recent releases of the XYLab have a new function for writing a debug file while running You can activate it by hitting the ctrl q combination and a debug file XYLab log will be written in the same location where the X YLab conf is placed When reporting bugs please inc
8. everything not responding to ribosomal should not be plotted and exactly 63 big red points should be present in the plot Now you can play with axes and look at ribosomal proteins move in their multidimensional space This is because the Label selector is on Annotation and you re not changing it If you change this you change the dataset on which the ribosomal filter is applied Now press the Unlock function it switches the XYLab to Lock mode This means that the selection of ribosomal protein is maintained also if you change the Label selector Try to change it to Length Set X axis to gCAI and Y axis to CAI and place the mouse over the point with the highest Y value The pop up label should indicate 366 that is the length of that protein Now let s change to another topic Restore all controller buttons to green i e in Full and Unlock mode and select CAI as X axis and gCAI as Y axis Look at the two topmost points that are those in 3 Look at the zoom copy selector it is now on zoom mode Now zoom on those two points by drawing a rectangle around them with left mouse button pressed When the button is released the zoom is performed and you should see the two points isolated in the plot area Look at the axes they should be restricted to the selected area Now unzoom by clicking the right mouse button look at the plot it is restored to the previous one So left is zoom right is unzoom Now chan
9. g Single from the same menu Change the axes by playing with the axes selectors e g choose the same variable in both axes You should observe a straight line that bisects the plot area Not so informative I know Now play with the the X Y and Labels controllers to enjoy the XY Lab pop up capability in different situations Select Annotations for the Labels controller Now fill the Find string box with the term ribosomal and press Enter A number of points should grow in size and become red In the status bar placed at the bottom of the program window you should observe 63 elements found matching ribosomal Now change the label from the Labels controller choose NOST All the previously highlighted points should turn back to original shape and color This is because the NOST variable contain numerical values of normalized Codon Adaptation Index so it is evident that the term ribosomal cannot match anything inside that kind of variable Let s come back to 6 Instead of ribosomal specify ribosomal that in the XYLab syntax means everything but ribosomal You should reverse the highlight situation and all points but 63 should be highlighted the statusbar should say that 4177 elements does not match ribosomal since 4240 63 4177 Let s come back to 6 Press the Full button that turn from green to red indicating that the XYLab is in the Restrict mode This means that
10. ge the zoom copy selector to copy Repeat the operation in 11 i e draw a rectangle around the two topmost points In the current configuration you should get the CAI X gCAI Y and length of the two points in the paste area This is because of the axes selector s choice Change the Label selector to Annotation and repeat the mouse selection Now the information showed in the paste area should be different 14 From the menu select Copy and click on Full Repeat 12 Now the full variable set should be present in the paste area ready to be pasted elsewhere Take a look at what happened at point 5 Remember the Full in that case Same meaning in different situations This is a basic usage explained There are many other features that you ll have to experience with Feel free to contact me for any further explanation
11. ion Fina string _Untock ran Zoom Copy Control area elements Main data controllers zeon ll CS eean O gt Lebelsf y 1 X column data selector selects the column from which the x axis values are taken 2 Y column data selector selects the column from which the y axis values are taken 3 Labels data selector selects the column from pop up labels are taken Axis controllers min max Log Norm Std Cent Value min max restrict the axis range setting up the extreme values Log take the logarithm of the values inactive in case of any value lt 0 in the column Norm normalize the values between 0 and 1 Std standardize the values with zi vi avg stdev Cent center the data around an average of zero with c vi avg Value real time values referring to cursor position on the plot SS CON AM Mouse left button controller C Copy Zoom 10 Copy Zoom selector switch the mouse cursor mode between zoom mode and copy mode Find line Find string 11 Find string line where the find string is specified Find mode is activated when the Enter key is pressed Find controller 12 Lock Unlock button used to fix and unfix the highlighted results while changing the Label data selector 13 Full Restrict button used to plot all the entities or only the found ones Input file The XYLab input data is constituted by a plain text file containing tab separated dat
12. lude the dataset you use when the errors were generated and the corresponding debug file 00 0l 02 03 04 05 06 07 08 09 10 11 12 13 XY Lab basic usage explained on escherichia txt sample dataset Before launching the XYLab open the Escherichia txt file with a spreadsheet program e g Excel or with a text editor to familiarize with input format Note that the are 4240 lines that corresponds to points described by 18 different variables a total of 76320 data Launch the XY Lab by double clicking on the program icon Open the test dataset Menu Data Load Select the Escherichia txt file The plot should appear immediately shaped like an exponential curve X axis selector should be on CAT Y axis selector should be on gCAT while labels should be on Annotation Place the mouse on the point with the highest Y value in brief a label should pop up saying predicted stress response protein This is the functional annotation of that point Change the Labels selector to length and repeat what done in 3 The pop up label now should indicate 210 that is the length of that protein Play with this selector to explore the different labels associated with different points From the menu select Labels and click on Full Repeat 3 Now the full variable set is popped up This is a convenient way to control your dataset Now turn off Full by selectin
13. otation so no ribosomal keyword will match When specifying queries you can use the modifiers available in the Perl language For more info about pattern searching see the Perl manpages at http perldoc perl org perlre html and or http perldoc perl org perlreref html In addition you can specify three specific modifiers some_text tells the XYLab to show things that match some_text some_text tells the XYLab to show things that do not match some_text gt some_number tells the XYLab to show things whose values is higher than or equal to some_number lt some_number tells the XYLab to show things whose values is lower than or equal to some_number Obviously if you search numbers in text based labels or vice versa you could expect strange results and please avoid doing that To overcome the problem of missing pre found entities when changing the annotation column you can lock the search results thanks to the dedicated button The button turns red meaning that the highlighted entities will be the same even if you change the Label column In other words with lock you decide that you re interested in these entities no matter the X Y or Labels you ll use later To unlock simply press the Lock Unlock button again If you re really interested in the locked entities only you can force the plot area to restrict the visualization to that entities only This option is turned on off by the dedicated but
14. ton When data are fixed and restricted you can look at them moving in their multivariate environment with the preferred labels wow it is like to explore three dimensions maintaining a fixed fourth dimension The select n paste procedure The mouse controller in the control area allows you to switch on a very useful tool of the XYLab when Copy is on no zoom is possible but the same procedure used for zooming is used for selecting points in the plot When the left button is released the X Y and Label values of the selected points will be pasted in the copy paste area of the program You can freely edit this area by hand and save its content to a text file with the menu Copy gt Save copy buffer The copy paste procedure can be controlled with the Copy menu in single mode only the currently selected X Y and Label values will be pasted while in Full mode the whole feature set will be pasted Adjusting the visualization The plot area can be conveniently resized by using predefined shortcuts holding down the Alt key on the keyboard makes the arrow keys become size manager for the plot area see table below The amount of variation associated with arrows depends on the specific configuration see the X YLab conf section below Alt Ctrl Increase plot width Increase x axis margin Decrease plot width Decrease x axis margin t Increase plot height Increase y axis margin 1 Decrease plot height Decrease y
Download Pdf Manuals
Related Search