CYT-class {CytoTree} | R Documentation

## Class `CYT`

### Description

All information stored in CYT object. You can use `creatCYT` to create an CYT object. In this package, most of the functions will use CYT object as input, and return a modified CYT obejct as well.

### Slots

`raw.data`

  matrix. Raw signal data captured in flow or mass cytometry.

`log.data`

  matrix. Log-transfromed dataset of raw.data.

`meta.data`

  data.frame. Meta data information, and colnames of "stage" and "cell" are required.

`markers`

  vector. Markers used in the calculation of PCA, tSNE, diffusion map and UMAP.

`markers.idx`

  vector. Index of markers used in the calculation of PCA, tSNE, destiny and umap.

`cell.name`

  vector. Cell names after performing downsampling.

`knn`

  numeric. Numbers of nearest neighbors

`knn.index,knn.distance`

  matrix. Each row of the `knn.index` matrix corresponds to a point in `log.data` and contains the row indices in `log.data` that are its nearest neighbors. And each row of the `knn.distance` contains the distance of its nearest neighbors.

`som`

  list. Store som network information calculated using `FlowSOM`.

`cluster`

  data.frame. Cluster information

`pca.sdev,pca.value,pca.scores`

  PCA information of CYT object which are generated from `fast.prcomp`.

`tsne.value`

  matrix. tSNE coordinates information. See `Rtsne`.

`dm`

  DiffusionMap object. Diffusion map calculated by package `destiny`

`umap.value`

  matrix umap coordinates information calculated using `umap`.

`root.cells`

  vector, Names of root cells, which can be modified by `defRootCells`. A root cell is manually set to be the origin of all cells. Pseudotime in root cells are the lowest.

`leaf.cells`

  vector. Names of leaf cells, which can be modified by `defLeafCells`. A leaf cell is manually set to be the terminal state of all cells. Pseuodtime in leaf cells is the largest.

`network`

  list. Network stored in the calculation of trajectory and pseudotime.

`walk`

  list. Random forward and backward walk between `root.cells` and `leaf.cells`.

`diff.traj`

  list. Differentiation trajectory of all cells.

`plot.meta`

  data.frame. Plot meta information for `plot2D` or `plot3D`.

`tree.meta`

  data.frame. Tree meta information of CYT object.

[Package CytoTree version 1.0.3 Index]