Description Usage Arguments Details Value Author(s) See Also Examples

plot spike known concentration and measured intensity of one array.

1 2 3 4 5 6 | ```
plotSpikeCI(spike, parameter,array = 1, bc = FALSE, area = TRUE,
meanpoint = TRUE,xlab = "log(Concentration)",
ylab = "log(Intensity)", main = colnames(spike$R)[array],
onlycalib = TRUE, xlim = NULL, ylim = NULL, pch = 19,
cex = 0.2, meanpch = 21, meancex = 1, lwd = 1.5,
cy5col = "red", cy3col = "green", ...)
``` |

`spike` |
a |

`parameter` |
a |

`array` |
integer giving the array to be plotted. |

`bc` |
a logical value. |

`area` |
a logical value. |

`meanpoint` |
a logical value. |

`xlab` |
a title for the x axis. |

`ylab` |
a title for the y axis. |

`main` |
an overall title for the plot. |

`onlycalib` |
a logical value. |

`xlim` |
the x limits (min,max) of the plot. |

`ylim` |
the y limits of the plot. |

`pch` |
a integer code for one of plotting characters or symbols for the spike data set. Default is 21. |

`cex` |
a numerical value giving the amount by which the points which indicate spike data set should be scaled relative to the default. Default is 0.4. |

`meanpch` |
a integer code for one of plotting characters or symbols for the meanpoints. Default is 21. |

`meancex` |
a numerical value giving the amount by which the meanpoints should be scaled relative to the default value. Default is 1. |

`lwd` |
width of the model curves. Default is 1.5. |

`cy5col` |
color of all symbols for cy5. Default is red. |

`cy3col` |
color of all symbols for cy3. Default is green. |

`...` |
other graphical parameters can be used in function |

The function plots spike concentration and measured intensity of one array.
array number is specified by the argument `array`

. It accepts the concentration
of given array from the agrument `spike`

, which is a `SpikeList`

object. The measured intensities are calculated from `spike`

. Four different ways can
be used to calculate the measured intensities. Arguments `bc`

and `area`

are
logical and their combinations are used for specifying the four differents ways.
`bc`

indicates using background correction or not. `area`

indicates multipling
spot area or not. The default value of these two arguments are `bc`

= FALSE and
`area`

= TRUE.

In order to help data visualization, meanpoints and model curve can be added
on the plot. And the arguments `meanpoint`

and `parameter`

are correspond to these.
The meadians of every group of measured intensities which have the same concentration
are shown on the polt if `meanpoint`

is true. Model curves of both dye are
shown if the arguement `parameter`

is specified after parameter estimation.

A plot is created on the current graphics device.

Hui Zhao

see graphic functions `plot`

, `par`

1 2 3 4 5 6 7 8 9 10 11 12 |

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