import scanpy.api as sc
/Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters
sc.settings.set_figure_params(dpi=80) # low dpi (dots per inch) yields small inline figures
The objects can be downloaded from ftp://ngs.sanger.ac.uk/production/teichmann/BBKNN/MouseAtlas.zip
Harmony was ran analogously to what was done in the pancreas demonstration notebook.
%load_ext rpy2.ipython
%%R
library(harmony)
/Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Loading required package: Rcpp warnings.warn(x, RRuntimeWarning)
adata = sc.read('MouseAtlas.subset.h5ad')
pca = adata.obsm['X_pca']
batch = adata.obs['sample']
%%R -i pca -i batch -o hem
library(harmony)
library(magrittr)
t1 = Sys.time()
hem <- HarmonyMatrix(pca, batch, theta=4)
t2 = Sys.time()
hem = data.frame(hem)
t2-t1
/Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 1/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: 0% 10 20 30 40 50 60 70 80 90 100% warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: [----|----|----|----|----|----|----|----|----|----| warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: * warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: | warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 2/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 3/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 4/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 5/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 6/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 7/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 8/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 9/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Harmony 10/10 warnings.warn(x, RRuntimeWarning) /Users/kp9/anaconda3/envs/orig/lib/python3.5/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Error in (function (x) : attempt to apply non-function warnings.warn(x, RRuntimeWarning)
Clustered for 134 iterations Clustered for 112 iterations Clustered for 99 iterations Clustered for 93 iterations Clustered for 93 iterations Clustered for 87 iterations Clustered for 90 iterations Clustered for 86 iterations Time difference of 19.38482 mins
sc.settings.verbosity = 3
adata.obsm['X_pca'] = hem.values
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.pl.umap(adata, color='Cell types')
computing neighbors using 'X_pca' with n_pcs = 50 finished (0:00:36.10) --> added to `.uns['neighbors']` 'distances', weighted adjacency matrix 'connectivities', weighted adjacency matrix computing UMAP finished (0:02:11.17) --> added 'X_umap', UMAP coordinates (adata.obsm)
sc.pl.umap(adata, color='sample')