arrayPlot {GLAD} | R Documentation |

The function `arrayPlot`

creates spatial images of shades of gray or colors that correspond to the values of a statistic for each spot on the array. The statistic can be the intensity log-ratio, a spot quality measure (e.g. spot size or shape), or a test statistic. This function can be used to explore whether there are any spatial effects in the data, for example, print-tip or cover-slip effects.

arrayPlot.default(Statistic, Col, Row, ArrCol, ArrRow, SpotCol, SpotRow, mediancenter=FALSE, col=myPalette("green","red","yellow"), contour=FALSE, nlevels=5, zlim=zlim, bar=TRUE, ...) arrayPlot.arrayCGH(arrayCGH, variable, mediancenter=FALSE, col=myPalette("green","red","yellow"), contour=FALSE, nlevels=5, zlim=zlim, bar=TRUE, ...)

`arrayCGH` |
Object of class `arrayCGH` . |

`variable` |
Variable to be plotted |

`Statistic` |
Statistic to be plotted. |

`Col` |
Vector of columns coordinates. |

`Row` |
Vector of rows coordinates. |

`ArrCol` |
Number of columns for the blocs. |

`ArrRow` |
Number of rows for the blocs. |

`SpotCol` |
Number of column for each bloc. |

`SpotRow` |
Number of rows for each bloc. |

`mediancenter` |
If `mediancenter=TRUE` , values of `Statistic` are median-centered. |

`col` |
List of colors such as that generated by `Palettes` . In addition to these color palettes functions, a new function `myPalette` was defined to generate color palettes from user supplied low, middle, and high color values. |

`contour` |
If `contour=TRUE` , contour are plotted,
otherwise they are not shown. |

`nlevels` |
Numbers of levels added by `contour` if `contour=TRUE` . |

`zlim` |
Numerical vector of length 2 giving the extreme values of
`z` to associate with colors `low` and `high` of
`myPalette` . By default `zlim` is the range of
`z` . Any values of `z` outside
the interval `zlim` will be truncated to the relevant limit. |

`bar` |
If `bar=TRUE` , a calibration color bar is shown to the right of the image. |

`...` |
Graphical parameters can be given as arguments to function
`image` . |

N.B. : Col takes the values in 1:arrayRow*SpotRow and Row takes the
values in 1:arrayCol*SpotCol

This function is very similar to the `maImage`

written by Sandrine Dudoit with added options `zlim`

and
`mediancenter`

.

An image is created on the current graphics device.

Philippe Hupé, http://www.curie.fr.

`image`

, `contour`

, `arrayPersp`

, `myPalette`

.

data(arrayCGH) pdf(file="arrayCGH.pdf",height=21/cm(1),width=29.7/cm(1)) arrayPlot(array2$Log2Rat, array2$Col, array2$Row, 4,4,21,22, main="Spatial Image of array CGH") dev.off() # object of class arrayCGH array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22)) class(array) <- "arrayCGH" arrayPlot(array,"Log2Rat", main="Spatial Image of array CGH")

[Package *GLAD* version 1.0.1 Index]