Rice Panicle Topology Toolbox for Matlab, Version 1, May 2006
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CONTENTS
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I. FEATURES
II. GETTING STARTED
III. DEMO
IV. REFERENCE TABLE, FIGURES AND DATA FILES
V. FUNCTIONS AND HELP
VI. REFERENCE
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I. FEATURES
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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.
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II. GETTING STARTED
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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).
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III. DEMO
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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.
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IV. REFERENCE TABLE, FIGURES AND DATA FILES
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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
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V. FUNCTIONS AND HELP
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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.
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VI. REFERENCE
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* 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.