prcurve {FateID} R Documentation

## Computation of a principal curve for a given dimensional reduction representation

### Description

This function computes a principal curve for a given dimensional reduction representation which is specified by component names of an object returned by `compdr` using the princurve package.

### Usage

```prcurve(y, fb, dr, k = 2, m = "cmd", trthr = NULL, start = NULL, ...)
```

### Arguments

 `y` clustering partition. A vector with an integer cluster number for each cell. The order of the cells has to be the same as for the columns of x. `fb` fateBias object returned by the function `fateBias`. `dr` list of dimensional reduction representations returned by the function `compdr`. `k` integer number for the dimension to be used. This dimension has to be present in `dr`. Default value is 2. `m` name of the dimensional reduction algorithms to be used for the principal curve computation. One of `lle`, `cmd`, `dm`, `tsne`, `umap`. Default value is `cmd`. Has to be a component of `dr`, i.e. previously computed by `compdr`. `trthr` real value representing the threshold of the fraction of random forest votes required for the inclusion of a given cell for the computation of the principal curve. If `NULL` then only cells with a significant bias >1 are included for each trajectory. The bias is computed as the ratio of the number of votes for a trajectory and the number of votes for the trajectory with the second largest number of votes. By this means only the trajectory with the largest number of votes will receive a bias >1. The siginifcance is computed based on counting statistics on the difference in the number of votes. A significant bias requires a p-value < 0.05. Default value is `NULL`. `start` integer number representing a specified starting cluster number for all trajectories, i. e. a common progenitor cluster. The argument is optional. Default value is `NULL`. `...` additional arguments to be passed to the low level function `principal_curve`.

### Details

The function computes a principal curve for each differentiation trajectory by considering only cells that are assigned to the trajectory with a significant fate bias >1 or at least `trthr` of the random forest votes, respectively.

For simulateneous computation and plotting of the principal curve, see function `plotFateMap`.

### Value

A list of the following two components:

 `pr` A list of principal curve objects produced by the `principal_curve` function from the princurve package. Each component corresponds to one differentiation trajectory giving rise to one of the target clusters from the `fb` object. `trc` A list of ordered cell IDs for each trajectory in `pr`.

### Examples

```
x <- intestine\$x
y <- intestine\$y
tar <- c(6,9,13)
fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL)
dr <- compdr(x,z=NULL,m="cmd",k=2,lle.n=30,tsne.perplexity=30)
pr <- prcurve(y,fb,dr,k=2,m="cmd",trthr=0.25,start=NULL)

```

[Package FateID version 0.2.0 Index]