Changelog
Source:NEWS.md
jazzPanda 0.2.3
Updated on June 24, 2025
Changes to the package include:
-
function
get_vectors()
:- Parameters
w_x
andw_y
have been removed. Spatial windows are now automatically determined per sample using a 5% buffer around the coordinate range. - Improved handling of genes that are only detected in a subset of samples. If a gene is not present in a sample, a zero-filled vector is used for that sample to maintain consistent vector lengths across samples.
- Parameters
-
function
create_genesets()
:- Parameters
w_x
andw_y
have been removed. Spatial windows are now computed per sample using a 5% buffer based on input coordinates. - Improved handling of genes that are only detected in a subset of samples. If a gene is not present in a sample, a zero-filled vector is used for that sample to maintain consistent vector lengths across samples.
- Parameters
-
function
compute_permp()
:- Parameters
w_x
andw_y
are no longer required. Spatial boundaries are now automatically derived per sample using a 5% buffer.
- Parameters
jazzPanda 0.2.2
Updated on February 23, 2025
Changes to the package include:
-
function
get_vectors()
:Input
x
can also be a named list now. This approach enables users to directly input transcript detection coordinates using a dataframe. This helps prevent integer overflow issues that may arise when creating the SpatialExperiment object for a large datasetIf invalid cluster/sample names are detected, the function
make.names()
will be employed to generate valid names. A message will also be displayed to indicate this change.
-
function
create_genesets()
:- Input
x
can also be a named list now as inget_vectors()
- Input
jazzPanda 0.2.1
Updated on January 20, 2025
Changes to the package include:
-
New Accessors for the Correlation Approach Results:
- Add the function
get_cor()
- Add the function
get_perm_p()
- Add the function
get_perm_adjp()
- Add the function
-
New Accessors for Results from the Linear Modeling Approach:
- Add the function
get_top_mg()
- Add the function
get_full_mg()
- Add the function
jazzPanda 0.2.0
Updated on November 16, 2024
To enhance interoperability with Bioconductor, the jazzPanda package has been updated to depend on the following data classes: SingleCellExperiment, SpatialExperiment, or SpatialFeatureExperiment.
Changes to the package include:
-
Removed Function:
- The
convert_data()
function has been removed from the export list.
- The
-
function
get_vectors()
:- Input
trans_lst
is renamed tox
. - Input
cm_lst
is removed. -
x
must be aSingleCellExperiment
,SpatialExperiment
, orSpatialFeatureExperiment
object. - Renamed
all_genes
totest_genes
to store genes for building spatial vectors.
- Input
-
function
compute_permp()
:- Input
data
is renamed tox
. -
n.cores
is renamed ton_cores
. -
x
must be aSingleCellExperiment
,SpatialExperiment
, orSpatialFeatureExperiment
object.
- Input
-
function
create_genesets()
:- Input
data_lst
is renamed tox
. -
x
must be aSingleCellExperiment
,SpatialExperiment
, orSpatialFeatureExperiment
object.
- Input
jazzPanda 0.1.1
Updated on November 12, 2024
- Add the
convert_data()
function to expand interoperability with Bioconductor. Support input objects from SingleCellExperiment/SpatialExperimentSpatialFeatureExperiment class - Modify one input type for function
get_vectors()
. Renamed input parameterdata_lst
astrans_lst
specifically for storing transcript coordinates only.