`degMDS.Rd`

Uses cmdscale to get multidimensional scaling of data matrix, and plot the samples with ggplot2.

degMDS(counts, condition = NULL, k = 2, d = "euclidian", xi = 1, yi = 2)

counts | matrix samples in columns, features in rows |
---|---|

condition | vector define groups of samples in counts. It has to be same order than the count matrix for columns. |

k | integer number of dimensions to get |

d | type of distance to use, c("euclidian", "cor"). |

xi | number of component to plot in x-axis |

yi | number of component to plot in y-axis |

ggplot2 object

data(humanGender) library(DESeq2) idx <- c(1:10, 75:85) dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx], colData(humanGender)[idx,], design=~group) degMDS(counts(dse), condition = colData(dse)[["group"]])