All information stored in FSPY object.
You can use `creatFSPY`

to create an FSPY
object. In this package, most of the functions will use
FSPY object as input, and return a modified FSPY obejct as well.

`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 FSPY 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`

. An 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`

. An leaf cell is manually set to be the terminal state of all cells. Pseuodtime in leaf cells are 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 all cells.

`plot.meta`

data.frame. Plot meta information for

`plot2D`

or`plot3D`

.`tree.meta`

data.frame. Tree meta information of FSPY object.

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