Rice Panicle Topology Toolbox for Matlab, Version 1, May 2006 ----------------------------------------------- CONTENTS ----------------------------------------------- I. FEATURES II. GETTING STARTED III. DEMO IV. REFERENCE TABLE, FIGURES AND DATA FILES V. FUNCTIONS AND HELP VI. REFERENCE ----------------------------------------------- I. FEATURES ----------------------------------------------- Encode Panicle Topology and Traits * Read panicle topology and trait data (panicle array) stored in tab-delimited text files. * Represent panicle as an annotated panicle array. Analyze Panicle Topology and Traits * Evaluate traits such as number of grains or branches. * Align annotated panicle arrays and compute a consensus. Visual Representation of Panicle * Graph annotated panicle array. ----------------------------------------------- II. GETTING STARTED ----------------------------------------------- Transferring Toolbox to Computer * Copy files from the zipped folder “Rice Panicle Topology Toolbox” in DSpace to a directory on your computer. Adding Toolbox to the Path *In the Matlab command window, add the directory containing the toolbox to the search path using the Set Path dialog box from the File menu. Constructing Panicle Array * Array grains on a 96-well plate from left to right and bottom to top using rules for skipped wells (see reference). * In Excel, into each cell corresponding to a well, input the Boolean value of a grain trait (one or two) or a three if the well was skipped. * Save file as Text (Tab delimited). Reading Panicle Array * In the Matlab command window, run GETPM(FILENAME). ----------------------------------------------- III. DEMO ----------------------------------------------- Running the Demo * In the Matlab command window, run EXAMPLE. When the procedure pauses, strike any key to continue. Description of the Demo * A panicle array in t1.txt is imported, annotated, graphed, analyzed for some traits, aligned with 6 other annotated panicle arrays (t2-t7.txt), a consensus is computed, and the consensus is graphed. ----------------------------------------------- IV. REFERENCE TABLE, FIGURES AND DATA FILES ----------------------------------------------- Reproduction of Table and Figures * In the Matlab command window, run PAPER to reproduce the figures and a table in the reference. Panicle Arrays in Text Files: * Set 1: 101-105.txt * Set 2: 151-155.txt * Set 3: 201-205.txt * Set 4: T1-T8.txt * Set 5: M1-M8.txt * Set 6: B1-B8.txt ----------------------------------------------- V. FUNCTIONS AND HELP ----------------------------------------------- Functions for Creating an Annotated Panicle Array * GETPM reads a panicle array in a tab-delimited text file. GETPM(FILENAME) is an m x 12 array, where m is the number of rows used when arraying grains on 96-well plates from left to right and bottom to top. If elements of the top row(s) are empty, they are read as zero. * PVA annotates a panicle array. PVA(PANICLE ARRAY) is an annotated panicle array (row vector). Functions for Analyzing an Annotated Panicle Array * NFS counts the number of dense grains. NFS(ANNOTATED PANICLE ARRAY) is the number of dense grains. NFS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of dense grains in each row. * NS counts the number of grains. NS(ANNOTATED PANICLE ARRAY) is the number of grains. NS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of grains in each row. * NUMNODES counts the number of rachis nodes. NUMNODES(ANNOTATED PANICLE ARRAY) is the number of rachis nodes. NUMNODES(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of rachis nodes in each row. * NUMPBS counts the number of primary branches. NUMPBS(ANNOTATED PANICLE ARRAY) is the number of primary branches. NUMPBS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of primary branches in each row. * NUMSBS counts the number of primary branches. NUMSBS(ANNOTATED PANICLE ARRAY) is the number of secondary branches. NUMSBS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of secondary branches in each row. * PBNFS counts the number of primary dense grains. PBNFS(ANNOTATED PANICLE ARRAY) is the number of primary dense grains. PBNFS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of primary dense grains in each row. * PBNS counts the number of primary grains. PBNS(ANNOTATED PANICLE ARRAY) is the number of primary grains. PBNS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of primary grains in each row. * SBNFS counts the number of secondary dense grains. SBNFS(ANNOTATED PANICLE ARRAY) is the number of secondary dense grains. SBNFS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of secondary dense grains in each row. * SBNS counts the number of secondary grains. SBNS(ANNOTATED PANICLE ARRAY) is the number of secondary grains. SBNS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a column vector containing the number of secondary grains in each row. Function for Plotting an Annotated Panicle Array * DRAW draws an annotated panicle array. DRAW(ANNOTATED PANICLE ARRAY) is a panicle graph. Functions for Aligning Annotated Panicle Arrays and Generating a Consensus * ALIGN aligns annotated panicle arrays or annotated panicle arrays of panicle arrays in tab-delimited text files. ALIGN(ANNOTATED PANICLE ARRAY 1, 2, 3, ..., m) or ALIGN(FILENAME 1, 2, 3, ..., m) is an m x n array of m aligned annotated panicle arrays. * CONSENSUS generates the consensus of an annotated panicle array alignment. CONSENSUS(ANNOTATED PANICLE ARRAY ALIGNMENT) is a row vector with nonzero elements. ----------------------------------------------- VI. REFERENCE ----------------------------------------------- * Hay, J.O. and Spanswick, R.M. (2006) Computational analysis of rice (Oryza sativa L.) panicle topology and ripening. Seed Science Research, 16: 243-250.