Marked the function clustersDeltaExpression() as legacy: it has been replaced
with the function DEAOnClusters() in the package
Fixed minor bug in class AdvancedGDIUniformityCheck regarding third check:
was testing third highest GID value instead of second
Fixed bug in the function cellsUMAPPlot(): restored possibility of passing a
genes vector as genesSel parameter. Also updated the documentation about the
available genes selection methods
Fixed typo in error message
Fixed bug in function genesCoexSpace(): now primaryMarkers can have only a
single gene
Exported utility functions about names arrays: conditionsFromNames(),
niceFactorLevels(), factorToVector()
feature/add_condition_arguments_to_plot_functions
Now the following plot functions take in conditions explicitly, instead of just
instructions to determine them from the cells' names. The changes involved:
cellSizePlot(), ECDPlot(), genesSizePlot(),
mitochondrialPercentagePlot(), scatterPlot()
Added possibility to convert COTAN objects to/from SingleCellExperiment
objects. SCE objects created by the Seurat package are supported
Hardened arguments' checks for function UMAPPlot()
Solved issue with the function establishGenesClusters(): it was throwing an
error when one of the sub-lists in the groupMarkers argument did contain
only one element
Introduced new way to check for the Uniform-Transcript property of the clusters based on multiple thresholds calibrated so that the new method is more effective at describing really statistically uniform clusters
Functions cellsUniformClustering() and mergeUniformCellsClusters() have been
re-factored so to support new class hierarchy for UT checkers.
This allows user to select which method to use for the checks;
as of now the following methods are supported:
"SimpleGDIUniformityCheck""AdvancedGDIUniformityCheck"
Avoided issue with pdf file creation: file handle was not closed in case of errors
Added possibility of choosing number of features in seuratHVG()
Solved minor issue with with clusterization functions in cases when only one cluster was created
Made function heatmapPlot() more easy to use and in line with the rest of
the COTAN package
Now the method storeGDI() can take in the output data.frame from
the function calculateGDI()
Solved few minor issues with the vignette and changed a few default parameters
in cellsUMAPPlot(), pValueFromDEA() and findClustersMarkers()
Stopped function cellsUniformClustering() from saving the internally created
Seurat object due to possibly long saving times
Split the now deprecated function getNormalizedData() into two separated
functions: getNuNormData() and getLogNormData()
Re-factored function mergeUniformCellsClusters() to be more precise:
now it merges clusters starting from the most similar in latest batch and
also runs the merging in multiple steps adjusting gradually the GDI threshold
ranging from a very strict up to the user given ones.
Fixed minor bugs in functions GDIPlot() and clustersMarkersHeatmapPlot()
Added possibility to display UMAP plots of cells clusters, using the function
cellsUMAPPlot()
Updated the vignette to the most recent changes
Allowed user to set the ratio of genes above the threshold allowed in a Uniform Transcript cluster
Solved issue with usage checks about the torch library
Allowed user to explicitly opt-out from the torch library usage:
COTAN will avoid torch commands when the option "COTAN.UseTorch" is
set to FALSE
Added support for the torch library to help with the heavy lifting
calculations of the genes' COEX matrix, with consequent substantial speed-up,
especially when a GPU is available on the system
First release in Bioconductor 3.20
Refactored DEAOnCluster() to make it run faster.
Now clustering functions dump the GDI check results for all clusters
Changed default GDI threshold to 1.43
Added new input to mergeUniformCellsClusters() to allow proper resume of
interrupted merges
Added possibility to query whether the COEX matrix is available in a COTAN
object
Made checks more strict when adding a clusterization or condition
Increased reliability of clustering functions by improved error handling and by allowing retry runs on estimators functions
Speed-up of GDI calculation via Rfast package
Added possibility of using distance between clusters based on Zero-One matrix instead of DEA
Added average floor to logFoldChangeOnClusters() to dampen extreme results
when genes are essentially absent from a cluster.
Added method to handle expression levels' change via log-normalized data:
logFoldChangeOnClusters()
Minor fix in the import of operators to align to new version of roxigen2
Restored default adjustment method of pValueFromDEA() to "none"
for backward compatibility reasons
Solved issue with cleanPlots() when the number of cells exceeded 65536
Added methods to calculate the COEX matrix only on a subset of the columns
Now the function pValueFromDEA() returns the p-value adjusted for multi-test
Stopped using explicit PCA via irlba package: using BioConductor PCAtools::pca instead
First release in Bioconductor 3.19
Made passing clusterizations to COTAN functions more easy:
now all functions that take a COTAN object and a clusterization as input
parameters can also take a clusterization name
Added time-stamps to log entries when written on a log file
Fixed bug in the clustersMarkersHeatmapPlot function when given a
clusterization not matching the latest added to the COTAN object
Fixed issue with the highest possible resolution in seuratClustering()
function, needed when large datasets must be split in many clusters
Added new flag to the function cleanPlots() to suppress evaluation of the
PCA on the normalized data. In particular, this allows to reduce significantly
time spent within the function checkClusterUniformity()
Added initialResolution parameter to cellsUniformClustering(): it allows
users to specify the initial resolution used in the calls to
Seurat::FindClusters() method. It now uses the same default as Seurat
Added new method estimateNuLinearByCluster() that calculates nu ensuring
that its average is 1.0 in each given cluster
Added function reorderClusterization(): it reorders the given clusterization
so that near clusters have also near labels
The functions cellsUniformClustering() and mergeUniformCellsClusters() now
return the result of this new function
Separated p-value calculations from DEAOnClusters() into the new function
pValueFromDEA(). Those data.frames are no longer part of the list returned
by the functions DEAOnClusters() and mergeUniformCellsClusters()
Added function getClusters() to retrieve the wanted clusterization from the
cells' meta-dataset
Added function calculateGenesCE(): it returns the cross-entropy between
the expected absence of a gene reading against the observed state
Fixed minor issue with logThis() to file: it was always appending a new line
even when appendLF was set to FALSE
Now checkClusterUniformity() returns more GDI stats like the percentage of
genes above threshold or the last percentile of the GDI values
Revamped mergeUniformCellsClusters() to select in order all the the most
likely candidates pairs of clusters to merge. Provided new user parameter to
balance the merging of most possible candidates versus the time spent doing so
Improved dropGenesCells() method: it now retains all meta-data information
that is not related to the results of the other methods
Added zoomed UDE plot to cleanPlots() return. It suggests a possible
cut level for low UDE cells
Improved mergeUniformCellsClusters(): now it attempts to merge more
clusters pairs
Now errors in the seuratClustering() function are interpreted as remaining
cells not-clustered "-1". This applies mostly to cases when Seurat finds only
singlets
Added flag calcCoex to proceedToCoex() and automaticCOTANObjectCreation()
functions to allow user not to spend time calculating the genes' COEX when not
needed
Solved potential issue in the clustersMarkersHeatmapPlot() regarding clusters'
labels
Added new internal function niceFactorLevels() that ensures all the factors'
levels will have labels with the same length, via padding the integers values
with '0' and string values with '_'
Relaxed tolerance on tests comparing against saved data
Speed-up by use of parallelDist::parDist() to calculate distances instead of
stats::dist()
Fixed regression tests failing on non-Linux architectures
Completed function clustersMarkersHeatmapPlot()
Added new utility function normalizeNameAndLabels()
Added mergeClusters() and multiMergeClusters() functions
Added support to conditions in cells' meta-data
Now clusterizations are stored as factors
Fixed COTAN::validity method in AllClasses.R
Fixed bug in proceedToCoex() in cases when saveObj == TRUE
Updated README.md and NEWS.md
Renamed methods dealing with housekeeping genes and fully-expressed cells to use the more proper names fully-expressed genes and fully-expressing cells
Added possibility to users to set the cutoff and thresholds used by the clean
and related methods
First release in Bioconductor 3.18
Solved remaining documentation warnings
Updated the vignette, README.md and NEWS.md
Dropped second vignette: will be merged in the other one...
Minor bug fixes and new function clustersMarkersHeatmapPlot()
Included new functionalities for Bioc 2.17 release:
-
created a new
COTANclass to replace the oldscCOTAN: this class provides internal invariants along a wide host of accessors that allows users to avoid peeking inside the class -
made a new multi-core implementation of the model parameters estimations and
COEXcalculations that achieves much higher speeds. -
added new functionality about gene clusters starting from given markers lists
-
added new functionality about uniform cell clustering based on the maximum GDI level in the cluster
-
added function to get a differential expression estimation for each cluster against background
-
added function to get an enrichment score for each cluster given a list of markers specific for the cells' population
-
added plots to asses data-set information at cleaning stage
After official release. PCA function changed to avoid basilisk and Python.
Release before the official release of Bioc 3.15. Main changes:
- The way in which the COEX matrix is estimated and stored is changed to occupy less space and run faster.
Initial Bioconductor release