Description Usage Arguments Examples

Plots the percentage of variance explained by the each component based on PCA from the normalized expression data using the same procedure used in reduceDimension function.

1 2 3 |

`cds` |
CellDataSet for the experiment after running reduceDimension with reduction_method as tSNE |

`max_components` |
Maximum number of components shown in the scree plot (variance explained by each component) |

`norm_method` |
Determines how to transform expression values prior to reducing dimensionality |

`residualModelFormulaStr` |
A model formula specifying the effects to subtract from the data before clustering. |

`pseudo_expr` |
amount to increase expression values before dimensionality reduction |

`return_all` |
A logical argument to determine whether or not the variance of each component is returned |

`use_existing_pc_variance` |
Whether to plot existing results for variance explained by each PC |

`verbose` |
Whether to emit verbose output during dimensionality reduction |

`...` |
additional arguments to pass to the dimensionality reduction function |

1 2 3 4 5 6 | ```
## Not run:
library(HSMMSingleCell)
HSMM <- load_HSMM()
plot_pc_variance_explained(HSMM)
## End(Not run)
``` |

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