What’s new in the package
A catalog of new features, improvements, and bug-fixes in each release.
v0.2.1 (November 6th, 2014)
This is a patch release, with non-breaking changes from v0.2.0.
v0.2.0 (November 5th, 2014)
This is a minor release, with some breaking changes from v0.1.1.
New features
- Plot the expression or splicing of two samples with
Study.plot_two_samples()
- Plot the expression or splicing of two features with
Study.plot_two_features()
- Detect outliers with Study.interactive_choose_outliers() which
performs a OneClassSVM on the PCA-reduced space of data (either
expression or splicing), using the first three components
- Study doesn’t filter out the pooled or outlier samples from the
data, only technical outliers with fewer reads than specified in the
argument mapping_stats_min_reads.
- To filter expression or splicing data on the number of samples that must
detect each feature, you can specify expression_thresh, and
metadata_min_samples in the Study constructor.
- For example, if expression_thresh=1 and metadata_min_samples=3,
then we will only take genes which have expression values greater than
1 in at least 3 samples. Additionally, we will also take splicing events
which were detected in at least three cells, since
metadata_min_samples applies to all data types.
API changes
- The attribute data in BaseData (i.e.
BaseData.data) now contains all the data, including pooled,
singles, and outliers
- The attribute data_original in BaseData (i.e.
BaseData.data_original) contains the original, unfiltered
data. For example, before removing features detected in fewer than 3 samples
with expression > 1.
- BaseData now has the attributes
BaseData.singles, BaseData.pooled, and
BaseData.outliers which are on-the-fly subsets of
BaseData.data. This is to maintain data provenance, meaning if
“outliers” is changed, this is also changed.
- In Study, you now must specify expression_feature_rename_col,
splicing_feature_rename_col, mapping_stats_number_mapped_col
explicitly, they are no longer defaulting to,
{splicing,expression}_feature_rename_col="gene_name" and
mapping_stats_number_mapped_col="Uniquely mapped reads number"
Other Changes
- Status messages in embark() have been moved to stdout instead
of stderr to avoid confusion that something is going wrong
- In embark(), user gets notified which samples are removed for having
too few reads (default minimum number of reads is \(5\times 10^5\), or
half a million reads).