CraneFoot v3.2 user's guide
Contents
1. A color is defined as a six digit integer with the first two digits denoting the red component intensity the next two denoting green and the last two denoting blue Patterns are also coded as integers but there is no obvious logic since the patterns themselves are quite different from each other except that the values range from 1 to 99 Figure 2 depicts some colors and all the available filling patterns 100000 11 d 22 pd 53 O 1 0o29 T 12 33 a 54 A2 109900 13 P 34 Be c da 3 009999 H u D m O 4 505050 Ej 2 m 2 H s Ws 290000 2 E s P V 6 290099 a 23 m E x O7 999900 A 24 Z s 3 8 999999 3 Ma 52 Figure 2 A list of some symbol colors and all pattern and shape codes In addition to color and filling pattern the individuals can be labeled by a diag onal slash SlashVariable a common glyph for death by a red arrow head ArrowVariable used for probands and by square brackets around the in dividual s name TracerVariable All the above are binary in nature and work similarly Any positive integer will draw the glyph in question otherwise it is not drawn Finally textual information can be attached to any individual by one or more TextVariables Each text variable specifies a data column and the particular text segment in the column will be printed below the individual s symbol Crane Foot is able to adjust the horizontal and vertical space so you can use any number of segments of any l2. 27 Lyn2 32 3 1 3 2 2 1 2 1 1 2 1 2 1 0 1 0 Lyn2 38 Lyn2 39 Lyn2 40 Lyn2 41 lLyn2 34 Lyn2 35 Lyn2 36 Lyn2 37 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 0 0 1 0 1 1 1 2 1 o 0 2 1 o 1 o 0 2 1 DISEASE DEAD ies Risk AQ NAME NO_DATA rion FE mia 0 GTYPE_A GTYPE_B P gt INDEX O w moderate Figure 3 Page layout in CraneFoot s primary output file The family name and size are on the top with date stamp and page number on the top right The legend is either on the left or if it is more space efficient on the bottom as in this case
3. input file for each drawing you can just change the instructions without manipulating the input files and thus save valuable time The third generation of CraneFoot suffers slightly from the indeterministic algo rithm that creates somewhat different layouts every time but in most cases you can circumvent this by using the RandomSeed instruction It will ensure that the positions on the canvas remain the same for each run provided that the textual features and page properties do not change Other useful instructions are listed in the last section Configuration interface File parameters PedigreeNam Template name for output files lt pedigreename gt _ lt family gt eps for fam ilies lt pedigreename gt ps for pedigree document and lt base gt topology txt for the topology file PedigreeFil required Pedigree data Must contain name father and mother columns Structural parameters AgeVariable Determine the order of siblings in the pedigree For a given nuclear family the oldest siblings are placed on the left FatherVariable required in pedigree file Father identification GenderVariable Gender data Cannot be used simultaneously with ShapeVariable MotherVariable required in pedigree file Mother identification NameVariable required Unique name for each individual for identification SubgraphVariable Family identification Visualization parameters ArrowVariable Black arrowhead pointing
4. path that you can type in the prompt If your file path contains space characters surround it with double quotes For example if you have c pedigree project 1 type cd c pedigree project 1 to enter the directory Linux UNIX installation Before you can start using CraneFoot on other than Windows systems you have to unpack the source code and combile it to a binary executable In most UNIX based systems the compiler software is already installed CraneFoot is written in C C and usual commands for a C compiler include c and g the latter is associated with the GNU compiler which is usually a safe choice To make the executable unpack the installation package unzip or similar go to the source directory and type g O5 o cranefoot main cc cpp lm to invoke the compiler When it finishes you should have a new file cranefoot in the directory To test the software move the file to the example directory and type Cranefoot config txt You should get two new files a PostScript file myPedigree ps and a text file myPedigree topology txt CraneFoot is a stand alone executable with no links to shared or dynamic li braries Furthermore you do not need any other files to run the program If you have root privileges you can copy the executable that you compiled to a location that is part of the execution path e g usr local bin Otherwise you can ask the system administrator to do that for you
5. CraneFoot v3 2 user s guide Ville Petteri M kinen Laboratory of Computational Engineering Helsinki University of Technology December 6 2006 Getting started Windows installation CraneFoot is a command line software and as such not very well suited for users who are accustomed to graphical user interfaces There is however a web based interface on the CraneFoot home page that makes the drawing of pedigrees easier but for practical reasons this option might not offer the same features as a proper installation 1 Unpack the installation package using WinZip or equivalent usually it is enough to just double click the icon It is highly recommended that the unpacked executable cranefoot exe and the exemplary data files are are at this point copied to a folder such as c cf3 so that they are easy to access from the command prompt You can find these files from the win32 and example folders within the installation package 2 Open the command prompt from the accessories leaf in the start menu Now proceed to the directory where you unpacked the executable and test Crane Foot by typing ed ce ct3 cranefoot config txt Press the return key after both lines to invoke the commands You should get two new files into the current directory a PostScript file myPedigree ps and a text file myPedigree topology txt Next create a new directory to another location for example c cf_test Copy the tw
6. You can also use the exe cutable directly through the full path If it is in the current directory just type cranefoot or if it is in your home directory e g home username type home username cranefoot Basic use CraneFoot is designed to be compatible with the so called linkage format where family relations are represented by a set of child father mother triplets As a result the natural format for the pedigree file is tabulated text with three columns de noted by NameVariable FatherVariable and MotherVariable One of the goals in the development of CraneFoot was to create a software with as little manual formatting of the input files as possible Hence the order and indeed the location of the columns in the file is irrelevant CraneFoot can detect them by itself if properly instructed Instructions are the human interface of CraneFoot In fact you do not submit the pedigree data directly to the software rather you give it a list of instructions that specify where to find the data how to read it and where to store the results The only requirement is that the data file is tabulated by a delimiter character and the first row contains unique names for each column a common description of a spreadsheet To draw a pedigree you need at least five instructions PedigreeFil pedigree txt PedigreeNam myPedigree NameVariable NAME FatherVariable FATHER MotherVariable MOTHER PedigreeFile contains the file path to
7. ates which is necessary if you want to draw the figure yourself based on the layout from CraneFoot The PostScript file with the suffix ps has three parts First a table of contents shows every successfully drawn subgraph of the entire data set then a list of errors is printed and finally the figures themselves on separate pages In this case we have just one subgraph with a generic name family we will shortly discuss how to partition the data into separate families Furthermore there were no errors and thus the second part is omitted The result is depicted on Figure 17 Sometimes it is useful to have a clean image of each subgraph in separate output files The encapsulated Postscript files eps depict only the subgraphs themselves without any extra information and you can use FigureLimit and PageSize to control the process Z FEL OOO Lyn2 22 wry Lyn2 25 Lyn2 19 Htz3 Htz3 8 Btz3 7 V gt 0 9 L Lyn2 28 Lyn2 27 Hez3 16 Htz3 15 Htz3 13 Lyn2 1 Lyn2 0 Xvj1 3 Xvj1 2 Htz3 6 Sto S E Lyn2 8 Lyn2 9 Lyn2 10 Xvj1 14 a d I oO lt Oo Lyn2 26 Lyn2 25 Lyn2 23 Lyn2 32 Lyn2 31 Lyn2 27 AS NA N xvj1 6 wa Lyn2 37 Lyn2 36 Lyn2 35 Lyn2 34 Figure 1 A clip from the basic drawing of the sample pedigree in pedigree txt Notice that CraneFoot automatically sets parents gender based on topology even if no gender information is available In genetic studies it is often t
8. ength Now that the main features have been covered it is time to put them to prac tice First let s examine some of the instructions in config txt in detail The GenderVariable has two values the column where the data is stored and the file where the column is stored By opening the file phenotypes txt you can see that it contains the name column NAME that is needed in identifying the rows and a column named GENDER as specified by the gender variable Simi larly two of the text variables point to two columns in another auxiliary input file genotypes txt The order of the lines of text that will be written below the nodes is determined by the order in which the text instructions are given Therefore the first Text Variable points to the name column just to ensure that the first piece of text is the individual s name Also remember from the previous discussion that it is not necessary to use multiple input files here it is done just as an example Next try removing the comment character to activate the visualization instruc tions to see what happens Figure 3 at the end of the document It should be clear by now that the instruction interface is a powerful tool to choose different visual izations from a collection of data For example you could have several datasets from the same pedigree each with a different set of individuals and you want to create visualizations from different points of view Instead of making a new
9. he case that you have a number of small pedigrees of The figure may not be exactly what you got due to the indeterministic layout algorithm unrelated families It is therefore important to treat them separately and for that purpose you can use the SubgraphVariable to name each family and to draw them on separate pages Try removing the comment character at the subgraph instruction in the sample file config txt and running CraneFoot again you should get a rewritten output document with multiple pages Note that a subgraph of one individual is not considered a proper family Using multiple input files Before going any further it must be emphasized that you need not put your data in multiple input files you can use just one This feature is optional and intended for cases where the user wants to integrate information from multiple sources when drawing a pedigree For example you can have extensive historical knowledge of a pedigree but you receive clinical information on only a handful of individuals Often it is prudent to combine the data into a single file but CraneFoot can do that for you if necessary Previously it was stated that the location of a particular variable i e column is of no consequence to CraneFoot if the heading is correct On that note the flexibility can still be increased if users can define the source file for each variable In order for this to work there has to be enough information to associate an i
10. ize Keyword for page sizes for the output documents Possible choices are letter and aQ to a5 for the first value main document The second value refers to the family outputs eps files with an additional option of automatic size auto The defaults are letter and auto for the first and second value respectively VerboseMode If off runtime messages are suppressed The default is on Delimiter The character that separates the columns in the pedigree file Use tab for the horizontal tabulator and ws for white space The default is tab BackgroundColor Six digit color definition for the canvas background The default is 999999 white ForegroundColor Six digit color definition for the general line art The default is 000000 black TimeLimit Maximum allowed time to spend on layout search This is not a hard limit If there are multiple small families or the families are very large the limit might not hold The default is 5s per family FigureLimit Maximum number of separate family outputs eps files The default is 0 RandomSeed Starting value for the pseudo random number generator that is used when computing the layouts If active TimeLimit is ignored 12 Lyn2 Jan 15 2006 42 individuals 2 10 N Lyn2 16 Lyn2 17 Lyn2 18 Lyn2 26 Lyn2 25 Lyn2 23 1 1 1 2 1 1 3 1 3 1 3 1 Lyn2 20 Lyn2 24 Lyn2 11 Lyn2 12 Lyn2
11. ndividual in the main pedigree file with a row in an auxiliary input file The only way to accomplish this is to make sure that every input file contains a name column that is a column with a heading specified by NameVariable A second condition is that the father and mother variables must be in the pedigree file this is merely a technical convenience Since the whole point of this feature is to add flexibility it is not mandatory to have the same individuals present in every input file In fact whether there are too many or too few individuals in a given input file compared to the pedigree file means only that some data on some individuals is missing it does not prevent the software from drawing the pedigree The next section on visualization features contains practical examples of using multiple files 3The default source file is defined by PedigreeFile Visualization features As is evident in Figure 1 information about the individuals sex should be given to CraneFoot so that children could be drawn properly The mechanism is the same as before You add a GenderVariabl1e instruction to the configuration file that tells which column contains the binary data You can set the character that corresponds to male female sex by using the instruction Male Female The default is M F The next two important features are the individual symbol color and filling pattern defined by ColorVariable and PatternVariable respectively
12. o main input files config txt and pedigree txt to this directory and then type Cd CNCE test c cf3 cranefoot config txt Again you should get the same output files You can use the previous com mand in any directory and supply any configuration file you want but make sure all the files you list in the configuration file are accessible Sometimes you may need to use full paths For instance suppose your data files are in c cfiles You could then write the instructions PedigreeFil c cfiles pedigree txt PedigreeNam c cfiles myPedigree in your configuration file the precise role of which is to be discussed in detail later Note that since the instructions are white space separated the paths must not contain white space characters It might also be necessary not to use directory names over 8 characters long There is a more elegant way of calling MS DOS programs and if the above method seems cumbersome try searching the Internet for path windows it should give enough links to relevant pages You should be able to cope with just two prompt commands cd target changes directory to target and dir shows the contents of the current directory The biggest problems in Windows come from the long and often compli cated file and directory names Use dir to see a shorter version of a file name that you can use as part of your commands You can also open the properties menu right click on an icon to look at the file
13. the primary input file In this case it is assumed that the file is in the current working directory hence the file name alone should suffice Note however that depending on your platform MS Windows in particular you may have to list the full path regardless of the file location As to PedigreeName CraneFoot needs to know where to save the results therefore you must provide a name for your pedigree that is used as a template for naming the output files At this point the most important thing to note is the freedom of choosing the name father and mother variables Although here the columns are named NAME FATHER and MOTHER they could be named differently for example ID FatID and MotID if so desired Even more significant is the lack of fixed location the mother column MotherVariable could be the first third or last column it makes no difference to CraneFoot as long as the column heading is consistent with the one provided in the configuration file The only restriction is that a heading must not contain white space characters since the configuration file must be white space delimited Assuming you have successfully installed and tested CraneFoot go back to the first section if not you should already have the output files myPedigree ps and myPedigree topology txt available The topology file is a printout of the logical relations between the individuals It also contains the symbol coordin
14. to the node drawn if integer value greater than 0 ColorInfo multiple Labels for specific colors Two value fields code and label Valid codes within 000000 999999 see Figure 2 ColorVariable Individual background color Valid codes within 000000 999999 see Fig ure 2 10 LabelVariable Node labels If none supplied individual names are used PatternInfo multiple Labels for specific patterns Two value fields code and label Valid codes within 1 99 see Figure 2 PatternVariable Individual patterns Valid codes within 1 99 see Figure 2 ShapeInfo multiple Labels for specific shapes Two value fields code and label Valid codes within 1 8 see Figure 2 ShapeVariable Shapes of pedigree nodes Valid codes within 1 8 see Figure 2 Cannot be used simultaneously with GenderVariable SlashVariable Diagonal slash drawn if integer value greater than 0 TextVariable multiple A line of text below a node TracerVariable Square brackets around the name drawn if integer value greater than 0 Formatting and functional parameters Female Alphanumeric code for the female sex The default is F FontSize Base font size The default is 10pt Male Alphanumeric code for the male sex The default is M PageOrientation Keyword for page orientation for the output document Possible choices are landspace and portrait The default is portrait 11 Pages
Download Pdf Manuals
Related Search