Produces two-dimensional plots of microarray data (D.B. Baird).

### Options

`SLIDES` = factor or text |
Defines the slides when the `X` and `Y` variates contain data from more than one slide |
---|---|

`SLIST` = variate or text |
Subset of slides to plot; default `*` i.e. all |

`GROUPS` = factor |
Specifies groups within slides |

`COLOURS` = text, scalar or variate |
Colours to use for the plots |

`SYMBOLS` = scalar or variate |
Symbols to use for the plots |

`REFERENCELINECHOICE` = string token |
Reference line to include (`identity` , `zero` , `none` ); default `none` |

`TRANSFORMATION` = string token |
Whether to transform data to logarithms base 2 (`log2` , `none` ); default `none` |

`SCALING` = string token |
Whether to use a common scale when not using Trellis plots (`common` , `none` ); default `comm` |

`BANDS` = string token |
Whether to plot approximate confidence bands (`confidence` , `none` ); default `none` |

`SMOOTHEDMEAN` = string token |
Whether to plot spline smooth of mean (`yes` , `no` ); default `no` |

`NROWS` = scalar |
Number of rows on a page in a trellis plot |

`NCOLUMNS` = scalar |
Number of columns on a page in a trellis plot |

`TITLE` = text |
Title for the graph |

`YTITLE` = text |
Title for the y-axis |

`XTITLE` = text |
Title for the x-axis |

`ARRANGEMENT` = string token |
Whether to use trellis, single or multiple plots when the `X` and `Y` variates contain data from more than one slide (`separate` , `overlaid` , `trellis` ); default `trel` |

`WINDOW` = scalar |
Window number for the graphs; default 3 |

`KEYWINDOW` = scalar |
Window number for the key; default 0 |

`DEVICE` = scalar |
Device number on which to plot the graphs |

`GRAPHICSFILE` = text |
What graphics filename template to use to save the graphs; default `*` |

### Parameters

`Y` = variates or pointers |
Y-coordinates |
---|---|

`X` = variates or pointers |
X-coordinates |

### Description

`MAPLOT`

produces two-dimensional plots of microarray data or transformed data using log base 2. The x- and y-coordinates are supplied, in variates or pointers, using the `X`

and `Y`

parameters, respectively. If you have data from several slides, you can set `DATA`

either to a list of variates, or to a pointer to the variates (one for each slide), or to a single variate containing the data from all the slides. When multi-slide data are in a single `DATA`

variate, the `SLIDES`

option must supply a factor to identify the slides. If they are in a pointer, the `SLIDES`

option can be omitted, or it can supply a text to identify the slides. By default, a plots are produced for the data from every slide, but you can set option `SLIST`

to a variate or text to define a subset of the slides to plot.

The `REFERENCELINECHOICE`

option allows you to include either an identity reference line or a horizontal reference at zero. The `BANDS`

option includes approximate confidence bands, and the `SMOOTHEDMEAN`

option adds a spline smooth of the mean. By default none of these are plotted.

The `COLOURS`

option can be set to a text, scalar or variate to define the colour(s) to use for the plots, and the `SYMBOLS`

option can be set to a scalar or variate to define the symbols. The `TITLE`

, `YTITLE`

and `XTITLE`

options can supply titles for the graph, the y-axis and the x-axis, respectively. The `WINDOW`

option specifies the window to use (by default 3), and the `KEYWINDOW`

option can specify a window for a key (by default there is none). You can use the `DEVICE`

option to plot to a device other than the screen. The `GRAPHICSFILE`

option specifies then supplies a template for the file names.

Options: `SLIDES`

, `SLIST`

, `GROUPS`

, `COLOUR`

, `SYMBOLS`

, `REFERENCELINECHOICE`

, `TRANSFORMATION`

, `SCALING`

, `NROWS`

, `NCOLUMNS`

, `TITLE`

, `YTITLE`

, `XTITLE`

, `ARRANGEMENT`

, `WINDOW`

, `KEYWINDOW`

, `DEVICE`

, `GRAPHICSFILE`

.

Parameters: `Y`

, `X`

.

### Action with `RESTRICT`

`MAPLOT`

takes account of any restrictions on `X`

, `Y`

or `SLIDES`

.

### See also

Procedures: `DMADENSITY`

, `FDRBONFERRONI`

, `FDRMIXTURE`

, `MACALCULATE`

, `MAESTIMATE`

, `MAHISTOGRAM`

, `MAPCLUSTER`

, `MASCLUSTER`

, `MASHADE`

, `MAVOLCANO`

, `MA2CLUSTER`

, `MNORMALIZE`

.

Commands for: Microarray data.

### Example

CAPTION 'MAPLOT example'; STYLE=meta ENQUIRE CHANNEL=-1; EXIST=check; NAME=\ '%GENDIR%/Data/Microarrays/Data13-6-9.gwb' IF check SPLOAD '%GENDIR%/Data/Microarrays/Data13-6-9.gwb' " Plot of Red vs Green Foreground on log2 scale in trellis plot." MAPLOT [ARRANGEMENT=trellis; SLIDES=Slide; GROUPS=Block; SYMBOL=1;\ BANDS=none; REFERENCE=identity; TRANSFORM=Log2]\ Y=F1_Mean; X=F2_Mean " Plot of logRatio vs Intensity, one slide per plot with approx confidence limits." MAPLOT [ARRANGEMENT=multiple; SLIDES=Slide; SYMBOL=1; SMOOTHEDMEAN=yes;\ REFERENCE=zero; BANDS=confidence; TRANSFORM=none; WINDOW=3]\ Y=logRatio; X=Intensity " Single overlaid Plot of logRatio vs Intensity." MAPLOT [ARRANGEMENT=single; SLIDES=Slide; SYMBOL=1;\ REFERENCE=none; TRANSFORM=none; WINDOW=1; KEYWINDOW=2]\ Y=logRatio; X=Intensity ELSE CAPTION 'Microarray example datasets have not been installed.' ENDIF