Description Usage Arguments Details Value See Also Examples

— Function in development, use with caution — Plot FlowSOM grid or tree, coloured by standard deviaton

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
PlotSD(
fsom,
marker = NULL,
view = "MST",
main = NULL,
colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan",
"#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),
symmetric = FALSE,
lim = NULL,
backgroundValues = NULL,
backgroundColor = function(n) { grDevices::rainbow(n, alpha = 0.3) },
backgroundLim = NULL,
backgroundBreaks = NULL
)
``` |

`fsom` |
FlowSOM object, as generated by |

`marker` |
If a marker is given, the sd for this marker is shown. Otherwise, the maximum ratio is used. |

`view` |
Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST) |

`main` |
Title of the plot |

`colorPalette` |
Color palette to use |

`symmetric` |
Plot colours symmetric around zero |

`lim` |
Variable limits |

`backgroundValues` |
Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering) |

`backgroundColor` |
Colorpalette to be used for the background coloring . Can be either a function or an array specifying colors |

`backgroundLim` |
Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues. |

`backgroundBreaks` |
Breaks to pass on to |

From suggestion in email: I am currently considering a way to summarize for each node all the SD as one value. After computing the SD matrix (nrow = # nodes, ncol = # markers), I compute the median value per column, then divide the SD matrix by it, and finally take the maximum ratio of each line (aka node). Doing so I got a unique dispersion score per node.

Nothing is returned. A plot is drawn in which each node is coloured depending on its standard deviation

`PlotMarker`

,`PlotStars`

,
`PlotPies`

,`PlotCenters`

,
`BuildMST`

1 2 3 4 5 6 7 8 | ```
# Read from file, build self-organizing map and minimal spanning tree
fileName <- system.file("extdata", "68983.fcs", package="FlowSOM")
flowSOM.res <- ReadInput(fileName, compensate=TRUE,transform=TRUE,
scale=TRUE)
flowSOM.res <- BuildSOM(flowSOM.res,colsToUse=c(9,12,14:18))
flowSOM.res <- BuildMST(flowSOM.res)
PlotSD(flowSOM.res)
``` |

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