Description Usage Arguments Value Examples

Given two distance matrices, the function categorizes one distance matrix and produces a box plot from the other distance matrix against the created categories. The option is available to choose one of the plots or to have both plots. The function also works on outputs from ADEC and CEC functions which do not have distance matrices but incidence matrices.

1 2 3 4 |

`Data1` |
The first data matrix, cluster outcome or distance matrix to be plotted. |

`Data2` |
The second data matrix, cluster outcome or distance matrix to be plotted. |

`type` |
indicates whether the provided matrices in "List" are either data matrices, distance matrices or clustering results obtained from the data. If type="dist" the calculation of the distance matrices is skipped and if type="clusters" the single source clustering is skipped. Type should be one of "data", "dist" or "clusters". |

`distmeasure` |
A vector of the distance measures to be used on each data matrix. Should be one of "tanimoto", "euclidean", "jaccard", "hamming". Defaults to c("tanimoto","tanimoto"). |

`normalize` |
Logical. Indicates whether to normalize the distance matrices or not, defaults to c(FALSE, FALSE) for two data sets. This is recommended if different distance types are used. More details on normalization in |

`method` |
A method of normalization. Should be one of "Quantile","Fisher-Yates", "standardize","Range" or any of the first letters of these names. Default is c(NULL,NULL) for two data sets. |

`lab1` |
The label to plot for Data1. |

`lab2` |
The label to plot for Data2. |

`limits1` |
The limits for the categories of Data1. |

`limits2` |
The limits for the categories of Data2. |

`plot` |
The type of plots: 1 - Plot the values of Data1 versus the categories of Data2. 2 - Plot the values of Data2 versus the categories of Data1. 3 - Plot both types 1 and 2. |

`StopRange` |
Logical. Indicates whether the distance matrices with
values not between zero and one should be standardized to have so. If FALSE
the range normalization is performed. See |

`plottype` |
Should be one of "pdf","new" or "sweave". If "pdf", a location should be provided in "location" and the figure is saved there. If "new" a new graphic device is opened and if "sweave", the figure is made compatible to appear in a sweave or knitr document, i.e. no new device is opened and the plot appears in the current device or document. Default is "new". |

`location` |
If plottype is "pdf", a location should be provided in "location" and the figure is saved there. Default is NULL. |

One/multiple box plots.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
## Not run:
data(fingerprintMat)
data(targetMat)
MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE)
BoxPlotDistance(MCF7_F,MCF7_T,type="cluster",lab1="FP",lab2="TP",limits1=c(0.3,0.7),
limits2=c(0.3,0.7),plot=1,StopRange=FALSE,plottype="new", location=NULL)
## End(Not run)
``` |

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