Description Usage Arguments Details Value Author(s) Examples

plot red intensity vs green intensity of spikes.

1 2 3 4 5 6 7 | ```
plotSpikeRG(spike,parameter,RG,array = 1, bc = FALSE, area = TRUE,
xlab = "log(Rintensity)", ylab = "log(Gintensity)",
main = colnames(spike$R)[array], onlycalib = FALSE,
xlim = NULL, ylim = NULL, pch = 19, cex = 0.3, col = "black",
allpch = 19, allcex = 0.05, allcol = "lightgrey", diag = TRUE,
diagcol = "grey", diaglwd = 1, curvecol = "blue",
curvelwd = 1.5, calibtype = 1, adjusttype = 4, ...)
``` |

`spike` |
a |

`parameter` |
a
If |

`RG` |
a |

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

`bc` |
a logical value. |

`area` |
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 (min,max) of the plot. |

`pch` |
an integer code for one of a set 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 0.3. |

`col` |
the color of the points indicating spike data set. Default is black. |

`allpch` |
an integer code for one of a set of plotting characters or symbols for the spike data set. Default is 19. |

`allcex` |
a numerical value giving the amount by which the points which indicate all data set should be scaled relative to the default. Default is 0.05. |

`allcol` |
the color of the points indicating all data set. Default is lightgrey. |

`diag` |
a logical value. Add diagonal on the plot if it is |

`diagcol` |
the color of the diagonal. Default is grey. |

`diaglwd` |
the width of the diagonal. Default is 1. |

`curvecol` |
the color of the model curves. Default is blue. |

`curvelwd` |
the width of the model curves for calibration control spikes. Default is 1.5. |

`calibtype` |
the line type of the model curves for calibration control spikes. Default is 1. |

`adjusttype` |
the line type of the model curves (using parameter after adjustment) for calibration control spikes. Default is 4. |

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

The function plots red vs green measured intensities of spikes of one array.
The argument `array`

gives the array index to be plotted.

If parameter estimation is done, the model curves can be plotted by giving
the argument `parameter`

. And if the argument `parameter`

is specified,
the argument `RG`

is obligated. The combination of these two arguments is
used to compare how the model fits to the spike and to the whole data set. More
details about the usage of this function refers to the readme file of this package.

It supports different ways to calculate the measured intensities.
Arguments `bc`

and `area`

are logical and their combinations are used
for specifying 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.

see other graphic functions for the other arguments.

A plot is created on the current graphics device.

Hui Zhao

1 2 3 4 5 6 7 8 9 10 11 12 13 |

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