Getting Started
Import Scimap as:
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Load Data
In order to make data analysis tools interoperable, scimap
has adopted the the AnnData
data structure. This allows users to use a wealth of single-cell analysis tools that works with AnnData structuring.
At the most basic level, an AnnData
object adata
stores a data matrix adata.X
, annotation of observations adata.obs
and variables adata.var
as pd.DataFrame
and unstructured annotation adata.uns
as dict. Names of observations and variables can be accessed via adata.obs_names
and adata.var_names
, respectively. AnnData objects can be sliced like dataframes, for example, adata_subset = adata[:, list_of_gene_names]
. For more, see the AnnData
page.
To initialize an AnnData object, the following can be performed.
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Note
If you used mcmicro pipeline to process your images, scimap
provides a handy function to convert mcmicro
output to AnnData
object.
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Work Flow
The typical workflow then consists of subsequent calls of scimap
tools:
Pre-Processing Tools under
sm.pp.<tool>
Analysis Tools undersm.tl.<tool>
Plotting Tools undersm.pl.<tool>
Helper Tools undersm.hl.<tool>