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.
matrix. Raw signal data captured in flow or mass cytometry.
matrix. Log-transfromed dataset of raw.data.
data.frame. Meta data information, and colnames of "stage" and "cell" are required.
vector. Markers used in the calculation of PCA, tSNE, diffusion map and UMAP.
vector. Index of markers used in the calculation of PCA, tSNE, destiny and umap.
vector. Cell names after performing downsampling.
numeric. Numbers of nearest neighbors
matrix. Each row of the
knn.index matrix corresponds to a point
log.data and contains the row indices in
log.data that are its nearest neighbors.
And each row of the
the distance of its nearest neighbors.
list. Store som network information calculated
data.frame. Cluster information
PCA information of FSPY
object which are generated from
matrix. tSNE coordinates information.
DiffusionMap object. Diffusion map calculated by package
matrix umap coordinates information
vector, Names of root cells, which can
be modified by
An root cell is manually set to be the origin of all cells.
Pseudotime in root cells are the lowest.
vector. Names of leaf cells, which can be
An leaf cell is manually set to be the terminal state of
all cells. Pseuodtime in leaf cells are the largest.
list. Network stored in the calculation of trajectory and pseudotime.
list. Random forward and backward walk between
list. Differentiation trajectory all cells.
data.frame. Plot meta information for
data.frame. Tree meta information of FSPY object.
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