Description Usage Arguments Value See Also Examples

View source: R/plotMRheatmap.R

This function plots a heatmap of the 'n' features with greatest variance across rows (or other statistic).

1 |

`obj` |
A MRexperiment object with count data. |

`n` |
The number of features to plot. This chooses the 'n' features of greatest positive statistic. |

`norm` |
Whether or not to normalize the counts - if MRexperiment object. |

`log` |
Whether or not to log2 transform the counts - if MRexperiment object. |

`fun` |
Function to select top 'n' features. |

`...` |
Additional plot arguments. |

plotted matrix

1 2 3 4 5 6 7 8 9 10 | ```
data(mouseData)
trials = pData(mouseData)$diet
heatmapColColors=brewer.pal(12,"Set3")[as.integer(factor(trials))];
heatmapCols = colorRampPalette(brewer.pal(9, "RdBu"))(50)
#### version using sd
plotMRheatmap(obj=mouseData,n=200,cexRow = 0.4,cexCol = 0.4,trace="none",
col = heatmapCols,ColSideColors = heatmapColColors)
#### version using MAD
plotMRheatmap(obj=mouseData,n=50,fun=mad,cexRow = 0.4,cexCol = 0.4,trace="none",
col = heatmapCols,ColSideColors = heatmapColColors)
``` |

metagenomeSeq documentation built on Nov. 1, 2018, 4:36 a.m.

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