NAME

SlideMap - Perl module for the creation of MicroArray slide maps

SYNOPSIS

use SlideMap;

$sm = SlideMap->new( machine => "arrayer", x_pin => 2, y_pin => 6,
					xspacing => 0, yspacing => 0, x_repeat => 1, 
					y_repeat => 1);

$sm->initialize;
$sm->fill_map;
$map_ref = $sm->getMap;

($array_row, $array_col, $meta_row, $meta_col, $sub_row, $sub_col) 
		= $sm->convert_well($plate_num, $well);

($plate_num, $well, $plate_row, $plate_col) 
		= $sm->convert_spot($array_row, $array_col);

($_meta_row,$_meta_col,$_sub_row,$_sub_col) 
		= $sm->get_meta($array_row, $array_col);
		
$sm->setMachine("arrayer");
$arrayer = $sm->getMachine;

$sm->setPrintHead(2, 6);
($x_pin, $y_pin) = $sm->getPrintHead;

$sm->setBlockDimensions(25, 24);
($x_spacing, $y_spacing) = $sm->getBlockDimensions;

$sm->setNoComplement([ 0 | 1 ]);
$noComplement = $sm->getNoComplement;

$sm->setRepeats([ 1 | 2 | 3 | 4 ], [ 1 | 2 | 3 | 4 ]);
($x_repeat,$y_repeat) = $sm->getRepeatMode;

$sm->setRepeatMode([ 0 | 1 ]);
$repeatMode = $sm->getRepeatMode;

$sm->setFormat([ 1 | 2 ]);
$plate_format = $sm->getFormat;

$sm->setPrintDirection([ 0 | 1 ]);
$direction = $sm->getPrintDirection;

$sm->setPlateOrder("[A,B,C,D,E,F,G ... | 1,2,3,4,5, ... ]");
$plate_order = $sm->getPlateOrder;

($max_array_row,$max_array_col) = $sm->getArrayDimensions;

($x_pitch,$y_pitch) = $sm->getPitch;

$number_of_spots = $sm->getNumSpots;

$sm->diagnostics;
$sm->print_spots([ 1 | 0 ]);
$sm->print_wells([ 1 | 0 ]);
$sm->showConvertWell;
$sm->showConvertSpot;

DESCRIPTION

SlideMap is used to create a row/col -> plate/well map of a microarray slide. It does not as yet incorporate annotation data into the map, but simply creates the map object based on input parameters. The map is an ordered list of spots with references to annonymous arrays containing array_row, array_col, plate_alias, well. SlideMap currently supports 5 types of arrayers: IAS (default), MD, MD3, Lucidia, and Stanford. (Others will be implemented as needed.)

SlideMap provides 2 methods for conversion of spots->wells and vise-versa, based on instantiated parameters.

The main parameters are: machine: the type of array printing machine used (IAS is the default) x_pin: the number of print head pens in the 'X' (plate_row) dimension y_pin: the number of print head pens in the 'Y' (plate_col) dimension (x_pin = 2, and y_pin = 6 are the defaults) x_spacing: the number of spots in one row of a block on the array y_spacing: the number of spots in one column of a block on the array (x_spacing = 24, and y_spacing = 25 are the defaults) x_repeat: the number of repeated block in the 'X' dimension (default = 1) y_repeat: the number of repeated block in the 'Y' dimension (default = 1)

The SlideMap module can be used in several ways: a) 'use' SlideMap, call the constructor with all parameters, and convert spots or wells, fill the map object and loop over it:

use SlideMap;
$sm->SlideMap->new( machine => "MD3", x_pin => 1, y_pin => 12,
			xspacing => 32, yspacing => 10);
$ref = $sm->fill_map;
foreach $row_ref (@$ref)) {
	($row,$col,$plate,$well) = @$row_ref;
	...
}

b) 'use' SlideMap, call the constructor with minimal parameters, and set parameters individually, then re-initialize and loop over the map:

use SlideMap;
$sm->SlideMap->new( machine => "MD3");
$sm->setBlockDimensions(32,6);
$ref = $sm->fill_map;
foreach $row_ref (@$ref)) {
	($row,$col,$plate,$well) = @$row_ref;
	...
}

c) 'use' SlideMap, call the constructor with machine argument not listed above, set parameters individuzlly, then initialize the map. This is useful for arrayers that are not listed above but operate similarly to one of the above mentioned machines. NOTE: default values for parameters are used in this case).

use SlideMap;
$sm->SlideMap->new(x_pin => 2, y_pin => 12, xspacing => 32, 
	yspacing => 10, machine => 'arrayer');
$sm->setNoComplement(1);
$sm->setFormat(1);
$sm->setPrintDirection(1);
$sm->setRepeats(1,1);
$ref = $sm->fill_map;
foreach $row_ref (@$ref)) {
	($row,$col,$plate,$well) = @$row_ref;
	...
}

There are several default values associated with each arrayer listed above. They are:

IAS: Default: format = 1 print_direction = 0 x_repeat = 1 y_repeat = 1 noComplement = 0

MD3: format = 2 print_direction = 1 x_repeat = 2 y_repeat = 1 x_spacing = 32 x_pin = 1 y_pin = 12 noComplement = 1

MD: format = 1 print_direction = 0 x_repeat = 2 y_repeat = 1 yspacing = 16 x_pin = 1 y_pin = 6 noComplement = 1

Stanford: format = 2 print_direction = 0 x_pin = 4 y_pin = 4 x_repeat = 1 y_repeat = 1 noComplement = 0

Lucidia: format = 2 print_dir = 1 x_repeat = 1 y_repeat = 1 nocomplement = 0 x_pin = 2 y_pin = 12

DETAILS

This constructor call will create a SlideMap object using the default parameter settings:

$sm = SlideMap->new( machine => "IAS", x_pin => 2, y_pin => 6, x_spacing => 24, y_spacing => 25, x_repeat => 1, y_repeat => 1);

The constructor will do all initialization, but will 'NOT' create a map in memory. That can be done as follows:

$sm->fill_map;

After the map has been created in memory, a reference to the map object is obtained by calling getMap. The map object is an array consisting of references to annonymous arrays holding array_row, array_col, plate_alias (or number), well number.

$map_ref = $sm->getMap;

Individual spots can be mapped back to their originating microtitre plate by supplying the row and column index of the spot to convert_spot:

($plate_num, $well, $plate_row, $plate_col) = $sm->convert_spot($array_row, $array_col);

Well is an integer representing the well position on a plate. Starting from well 1 (A1), this number increases across a row and then to the next row, so A12 in a 96-well plate is well 12 and B1 is well 13, etc. Plate_row is an 1-based integer that represents the row.

Likewise, the row and column indeces for a spot can be obtained from the plate_num and well used as source for the spot. NOTE: plate_num here refers to the position of the plate in the series of plates used for the printing, i.e. it is an plate ordinal.

@array_of_arrays = $sm->convert_well($plate_num, $well);

This method returns an array of references to arrays. Since a well may be spotted more than once on a slide (due to repeat status) this method returns data for multiple spots. Eeach reference points to an array with the following data:

($array_row, $array_col, $meta_row, $meta_col, $sub_row, $sub_col)

The meta_row and meta_col indeces refer to the row/col indeces of the pin that printed the spot in question. The sub_row and sub_col indeces refer to the indeces of the spot within a block. The array_row and array_col indeces are obvious.

SlideMap includes a convenience method to return the meta_row/col, and sub_row/col indeces for a pair of array_row, array_col indeces:

($_meta_row,$_meta_col,$_sub_row,$_sub_col) = $sm->get_meta($array_row, $array_col);

The following are get/set methods that can be used to customize a SlideMap object to accomodate array printers not supported at the time of release of SlideMap.pm.

getMachine: returns the current machine setting:

$arrayer = $sm->getMachine;

setMachine: sets the machine type used for printing. Currently SlideMap supports 4 types of arrayers: 'IAS', 'MD', 'MD3', 'Lucidia' and 'Stanford'. Note: This method resets all parameters to their pre-defined default values and reinitializes the SlideMap object. Using this methode requires that other parameters be set with the methods below (if they are different from the defaults). To set the machine type:

$sm->setMachine("arrayer");

setPrintHead: defines the numbers of pens in the print head, 'X' (plate_row) and 'Y' (plate_col):

$sm->setPrintHead(2, 6);

getPrintHead: returns the numbers of pens in the print head:

($x_pin, $y_pin) = $sm->getPrintHead;

setBlockDimensions: set maximumn row and column indeces in blocks on the array, row first then column:

$sm->setBlockDimensions(25, 24);

getBlockDimensions: returns block dimensions:

($x_spacing, $y_spacing) = $sm->getBlockDimensions;

NOTE: All of the following 'set*' methods require re-initialization of the SlideMap object:

$sm->initialize;

setNoComplement: switches printing pattern in the 'X' dimension; this is in effect complementing (1 - x) in the 'X' dimension only. Valid values are 0 => complemented, and 1 => 'NOT' complemented:

$sm->setNoComplement([ 0 | 1 ]);

getNoComplement: returns the current value of the noComplement parameter:

$noComplement = $sm->getNoComplement;

setRepeats: number of repeated blocks in 'X' and 'Y' dimension. Valid values are 1 - 4:

$sm->setRepeats([ 1 | 2 | 3 | 4 ], [ 1 | 2 | 3 | 4 ]);

getRepeatMode: returns the current values of x_repeat and y_repeat:

($x_repeat, $y_repeat) = $sm->getRepeatMode;

SlideMap supports repeat mode for the MD/MD3 arrayers only. setRepeatMode: normal mode ('0') does nothing, but repeat mode ('1') sets x_repeat = y_repeat = 1, and print_direction = 0 (like default):

$sm->setRepeatMode([ 0 | 1 ]);

getRepeatMode: returns the current value of the repeat parameter:

$repeatMode = $sm->getRepeatMode;

setFormat: microtitre plate format: valid values are 1 => 96-well, and 2=> 384-well:

$sm->setFormat([ 1 | 2 ]);

getFormat: returns the current value of the format parameter:

$plate_format = $sm->getFormat;

setPrintDirection: defines the order of printing used by the printer. Valid values are 0 => top->bottom, and 1 => left->right:

$sm->setPrintDirection([ 0 | 1 ]);

getPrintDirection: returns the current value of the print_dir parameter:

$direction = $sm->getPrintDirection;

setPlateOrder: define a list of plate labels (aliases) for the complete set of plates used for printing. The list should include all repeats of the plate:

$sm->setPlateOrder("[A,B,C,D,E,F,G ... | 1,2,3,4,5, ... ]");

getPlateOrder: returns a reference to an array containing the entire list of plate labels:

$plate_order_ref = $sm->getPlateOrder;

getArrayDimensions: returns the maximum row and column indeces for the current SlideMap object:

($max_array_row,$max_array_col) = $sm->getArrayDimensions;

getPitch: returns the pitch values used to create the current SlideMap object:

($x_pitch,$y_pitch) = $sm->getPitch;

getNumSpots: returns the number of spots in the current SlideMap object:

$number_of_spots = $sm->getNumSpots;

DIAGNOTICS

diagnostics: returns the full set of current values for the SlideMap parameters:

$sm->diagnostics;

print_spots/print_wells: prints an entire set of row/col/plate/well values based on the current SlideMap parameters. if the optional parameter is set to 1 (true) then well numbers are printed as well numbers; if set to 0 or not set, then the well number is returned as row_col, i.e. A1, B12, etc. These methods are useful for diagnosing errors in the print pattern.

$sm->print_spots([ 1 | 0 ]); $sm->print_wells([ 1 | 0 ]);

The algorithms used to convert spots to wells and vise-versa are dynamically generated based on the type of arrayer (machine) supplied as a parameter to the constructor (or to setMachine). To view the algorithm currently being used, use either of the following methods:

$sm->showConvertWell; $sm->showConvertSpot;

EXPORT

None by default.

AUTHOR

Joseph A. White; jwhite25@verizon.net Version 1.4 Aug 14, 2023

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