align_embedding_to_reference: Align simple (y-shaped) lineage trees represented as points...
In maehrlab/thymusatlastools: Tools for analysis of single-cell transcriptomic data
Description
Output from Monocle is arbitrarily rotated and reflected.
For bootstrap analysis where I call Monocle on subsets of the data, it's useful to
align all of the results so that cells are in roughly the same positions across bootstrap samples.
This program does that for any two matrices mat_ref and mat_samp.
Rows are cells and columns are dimensions of some embedding.
Usage
1
align_embedding_to_reference(mat_samp, mat_ref, do.plot = F)
Details
The reference and the query can have different numbers of columns.
They should have the same number of rows, or else
the property all( rownames( mat_samp )
The solution is based on linear regression.
The return value is a projection of each column of mat_ref onto the column space of the
augmented matrix [mat_samp | 1]. In other terms, mat_samp is translated and linearly combined to
minimize the l2 distance to each column of mat_ref, then returned.
This function always returns a numeric matrix with ncol = ncol(mat_ref) and nrow = nrow(mat_samp).
maehrlab/thymusatlastools documentation built on May 28, 2019, 2:32 a.m.
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Description
Output from Monocle is arbitrarily rotated and reflected. For bootstrap analysis where I call Monocle on subsets of the data, it's useful to align all of the results so that cells are in roughly the same positions across bootstrap samples. This program does that for any two matrices mat_ref and mat_samp. Rows are cells and columns are dimensions of some embedding.
Usage
1 | align_embedding_to_reference(mat_samp, mat_ref, do.plot = F)
|
Details
The reference and the query can have different numbers of columns. They should have the same number of rows, or else the property all( rownames( mat_samp ) The solution is based on linear regression. The return value is a projection of each column of mat_ref onto the column space of the augmented matrix [mat_samp | 1]. In other terms, mat_samp is translated and linearly combined to minimize the l2 distance to each column of mat_ref, then returned. This function always returns a numeric matrix with ncol = ncol(mat_ref) and nrow = nrow(mat_samp).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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