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output_width and
output_height to the Iterate_* family of
plotting functions (#217).Random_Cells_Downsample that prevented
setting identity using the group.by parameter.Cell_Highlight_Plot that didn’t pass the
reduction parameter properly (#216).return_plots in
iterative plotting functions(#217).Major Updates to Functionality with rliger
Package:
Added new utility functions to interact with liger v2.0.0+ object
format change:
- Subset_LIGER to quickly subset by cluster or other meta
data variable.
- Cells_by_Identities_LIGER to extract list of barcodes
sorted by values within given meta data column.
Extended the following Seurat/SeuratObject generic functions to
work seamlessly with liger objects:
- Cells to extract vector of all cells or list vectors of
cells by dataset.
- Features to extract vector of all features or list
vectors of features by dataset.
- WhichCells to extract vector or list of cells matching
identity criteria.
- Embeddings to extract matrix containing dimensionality
reduction embeddings or iNMF h.norm matrix.
- Idents and Idents<- to extract and set
default identities/clusters.
Updated functions to interact with both old and new style liger
objects:
- plotFactors_scCustom()
- Fetch_Meta
- Top_Genes_Factor
- Add_Mito_Ribo
- Add_Cell_Complexity
- DimPlot_LIGER
- Variable_Features_ALL_LIGER
- Feature_Present
New functions compatible with old and new style liger
objects:
- Added new function Add_Hemo to add hemoglobin gene
percentage for QC. Also added as parameter to
Add_Cell_QC_Metrics. Add_Hemo supports all
default species: (human, mouse, marmoset, zebrafish, rat, drosophila,
rhesus macaque, and chicken) and works with both Seurat and liger
objects.
New scCustomize generics to function across both Seurat and Liger
objects:
- Add_Hemo (see above).
- Rename_Clusters now S3 generic for setting new
active.ident (Seurat) or defaultCluster (Liger).
New functions for Seurat and rliger v2.0.0+ only:
- Added new function Find_Factor_Cor to return correlation
matrix between factor gene loadings from liger or Seurat object.
- Added new function Factor_Cor_Plot to plot positive
correlations from liger or Seurat object.
Updated functions to recommend new rliger equivalents for users
with rliger v2.0.0+:
- as.LIGER
- as.Seurat
General scCustomize Updates:
New functions:
- Added new function Add_Hemo to add hemoglobin gene
percentage for QC. Also added as parameter to
Add_Cell_QC_Metrics. Add_Hemo supports all
default species: (human, mouse, marmoset, zebrafish, rat, drosophila,
and rhesus macaque) and works with both Seurat and liger objects.
- Added new function seq_zeros() to create sequences with
preceding zeros.
- Added new function Read_Metrics_CellBender to read in the
summary metrics csv file produced by CellBender. Can either read all
metrics files from parent directory of output folders or a single
metrics file.
- Added Updated_MGI_Symbols to check for update gene
names/symbols in mouse data (#202).
- Added plotting function Proportion_Plot to plot pie chart
or bar chart of proportion (or total counts) of cells in each identity
class.
- Added new function Random_Cells_Downsample to return
either a vector or list with randomly downsampled cells for each
identity class.
- Added new function Cells_per_Sample to quickly return
data.frame with just number of cells per sample.
Updated functions:
- Added new parameters data_name and overwrite
to Add_Alt_Feature_ID to support new storage
location.
- Added cells parameter explicitly to
FeatureScatter_scCustom.
- Added Chicken (Gallus gallus) to default species for QC functions.
Thanks @dpearton;
(#176).
- Added new plotting function SpatialDimPlot_scCustom.
Thanks for encouragement @puapinyoying @nina-hahn (#160).
- Added ability of Read_Metrics_10X to read a single
metrics csv file and return data formatted the same way as when reading
multiple files.
- Added parameter cutoff_line_width to the
QC_Plot_* family of plots to control line thickness of
cutoff lines.
- Cluster_Stats_All_Samples now returns data.frame with row
order reflecting the frequency of cells.
- Add_Mito_Ribo now supports datasets aligned to
multi-species reference genomes (#184).
- Added parameter add_prop_plot to
DimPlot_scCustom to return plot showing number or percent
of cells per identity along with the DimPlot.
- Added optional parameter colors_use_assay2 to
FeaturePlot_DualAssay which allows for specification of
different palettes for the two plots (#182).
- Added new folder and scripts (see “data-raw/” on GitHub) detailing the
creation of gene lists used in Add_Cell_QC_Metrics.
- Added ensembl ID support for percent hemoglobin, msigdb, and IEG gene
sets (#186).
- Add verbosity parameter to Store_Misc_Info_Seurat and
Store_Palette_Seurat.
- Explicitly reveal the reduction parameter in
Cluster_Highlight_Plot and Meta_Highlight_Plot
(#198).
- Added show_row_names show_column_names,
column_names_side, row_names_side,
legend_position, legend_orientation,
show_ident_legend, and show_ident_colors
parameters to Clustered_DotPlot. Thanks for idea and code
@johnminglu (#199).
- Updated Split_Vector to allow user to specify number of
chunks or size of chunks for splitting vector.
- Update RenameClusters with additional parameters to
enable storage of both old idents and new idents in meta.data within the
function.
- Update Add_Cell_QC_Metrics.Seurat to explicitly reveal
list_species_names parameter.
- Added new vignette for spatial plotting.
- Added new and expanded vignette on use of object QC functions for
better clarity on these functions and their uses (previously was part of
QC Plotting & Helpers/Utilities Vignettes). Plotting elements of QC
Plotting vignette are unchanged.
Add_Top_Gene_Pct_Seurat is now S3 generic that works with
both Seurat and liger objects and has been renamed
Add_Top_Gene_Pct.Add_Cell_QC_Metrics is now S3 generic and works with
both Seurat and liger objects.Add_Alt_Feature_ID to
@misc slot of object for safer storage across object
filtering.as.anndata to explicitly check for
installation of anndata before starting conversion (#162).Plot_Median_Genes,
Plot_Median_UMIs, Plot_Median_Mito,
Plot_Median_Other, Plot_Cells_per_Sample to
understand “ident” as grouping variable.Store_Misc_Info_Seurat to use Seurat
accessor/setter function Seurat::Misc().sample_names in
Read_CellBender_h5_Multi_File to clarify parameter behavior
(related to (#208)).Read_Metrics_10X to support adjusts to metrics
summary format and metric names in output from Cell Ranger v9+.Plot_Density_Custom and
Plot_Density_Joint_Only have been re-enabled for users with
ggplot2 v3.5.0 following Nebulosa v1.12.1 update patch.Add_Cell_QC_Metrics when
overwrite = TRUE (#165).DotPlot_scCustom (#158).as.anndata from
Seurat conversion that previously caused failures (#168).Create_Cluster_Annotation_File if for
file path and csv name errors.plot_median and more than one
feature in VlnPlot_scCustom (#169).DimPlot_scCustom
due to changes in guides updated with ggplot2 v3.5.0 (#171).Add_Sample_Meta that still errored when
setting na_ok = TRUE.Plot_Median_* family that caused issues
when group_by parameter was NULL.FeaturePlot_scCustom when setting
combine = FALSE.DimPlot_scCustom that could cause blank
plot when rasterizing points.MAD_Stats that didn’t respect
mad_num parameter (#183).MAD_Stats that could cause issues if
mad_num was less than or equal to 0 and returned error if
setting group_by_var to “ident”.all_of/any_of syntax.Cluster_Highlight_Plot with split.by parameter
(#201).Convert_Assay (#205).Updated_HGNC_Symbols due to change in
URL path for gene names (#209).DimPlot_scCustom when
split.by and label.box = TRUE.DiscretePalette_scCustom that didn’t error
when supplying invalid palette names.DimPlot_LIGER that provided uniformative
error message when changing the default cluster ident.Plot_Density_Custom and
Plot_Density_Joint_Only due to error in Nebulosa following
ggplot2 v3.5.0 update. Functionality will be restored when Nebulosa
package is updated.as.liger that prevented function
from running properly.title_prefix parameter to
Iterate_DimPlot_bySample to unify with
Meta_Highlight_Plot.Split_Vector to split vector in chunks
of predetermined sizes.Updated_HGNC_Symbols to update human
gene symbols. After first use does not require internet
connection.Seurat::LogSeuratCommand().plot_legend to
plotFactors_scCustom to allow for removal to legend in
factor loading plots.Iterate_FeaturePlot_scCustom
to allow for plotting multiple plots per page when saving to single PDF
document (see new parameters: features_per_page and
landscape.LIGER_Features utility function for LIGER objects
(analogous to Seurat::Features()).as.LIGER() as enhanced method for
conversion of Seurat objects or lists of Seurat objects to single LIGER
object.as.anndata() to support conversion of
Seurat and LIGER objects to anndata format.Convert_Assay() to perform easy
conversions of Seurat assays between V3/4 (Assay) and V5 (Assay5)
formats.assay_type to allow manual control of
assay type when creating Seurat object from LIGER using
Liger_to_Seurat. Now as.Seurat.grid_color to
Clustered_DotPlot to control the color of grid lines
(default is no grid lines).Clustered_DotPlot
by additional variable and maintain expression information.Split_Layers() function for V5 objects.Add_Alt_Feature_ID to add alternative feature ids
to an Assay5 meta.data slot.Add_Mito_Ribo() replaces
Add_Mito_Ribo_Seurat and
Add_Mito_Ribo_LIGER.Add_Cell_Complexity() replaces
Add_Cell_Complexity_Seurat and
Add_Cell_Complexity_LIGER.Meta_Present_LIGER
has been deprecated and wrapped inside of
Meta_Present.Liger_to_Seurat() has been soft-deprecated. It is replaced
by new extension of Seurat generic as.Seurat with added
support for Liger objects, using all the same parameters as
Liger_to_Seurat. Full deprecation will occur in
v2.2.0.Gene_Present has been soft-deprecated. It is replaced by
Feature_Present which functions identically but better
reflects that features present may also be proteins. Full deprecation
will occur in v2.2.0.legend in
Iterate_DimPlot_bySample has been inverted to
no_legend to match Meta_Highlight_Plot
parameters.Liger_to_Seurat() for compatibility with Seurat
V5 structure (#153).
Now part of as.Seurat.Stacked_VlnPlot due
to rasterization defaults.alpha_na_exp appropriately in
FeaturePlot_scCustom.alpha_exp between Seurat versions 4
and 5 (#144).DimPlot_scCustom when levels
are missing from a split plot.FeaturePlot_scCustom that could cause
plots to be mislabeled when using split.by and depending on
the order of features provided (#150).DimPlot_LIGER (#153).Add_Mito_Ribo_LIGER that caused it to
return value of 0 for all cells (Now part of renamed
Add_Mito_Ribo S3 generic).Clustered_DotPlot to display
percentage instead of proportion to match legend text.Percent_Expressing error when
group_by = "ident".DotPlot_scCustom that didn’t correctly
pass group.by when plotting (#158).VariableFeaturePlot_scCustom now
fixed in Seurat release.Add_Mito_Ribo_Seurat causing failure due
to error message when overwrite = TRUE.Add_Top_Gene_Pct_Seurat to avoid issue
that accidentally could call function on normalized data.Add_Top_Gene_Pct_Seurat that caused
error if more than one counts layer was present.QC_Histogram that prevented plotting or
titling of plots.multi
pipeline to Read10X_Metrics via new parameter
cellranger_multi.dot_size parameter to Seq_QC_Plot_*
family of functions.Barcode_Plot and
Iterate_Barcode_Rank_Plot.ident_legend parameter to
QC_Plot_UMIvsGene to control show/hide of the identity
legend (#121).CellBender_Feature_Diff.min_count_label in
CellBender_Diff_Plot to better control feature
labeling.Iterate_DimPlot_bySample using new
sample_column parameter.MAD_Stats to calculate to the median
absolute deviation of meta.data columns by grouping variable and across
entire object.Add_Top_Gene_Pct_Seurat to add
another QC measure of cell complexity to object meta.data. Returns
percentage of counts occupied by top XX genes in each cell.VariableFeaturePlot_scCustom using
custom_features parameter.Add_Cell_QC_Metrics to simplify adding cell QC metrics.
Single function call to add Mito/Ribo Percentages, Cell Complexity, Top
Gene Percentages, MSigDB Percentages, IEG Percentages, and/or Cell Cycle
Scoring (human only).Add_Cell_QC_Metrics function: “msigdb_qc_gene_list” and
“ieg_gene_list”.Add_Cell_QC_Metrics.plot_median and
plot_boxplot to VlnPlot_scCustom (and
VlnPlot_scCustom-based plots; e.g., QC_Plot_*
family) for added visualization.QC_Histogram to plot QC features (or any feature)
using simple histogram.FeatureScatter_scCustom function to customize
Seurat’s FeatureScatter plots.figure_plot parameter to all 2D DR (t-SNE, UMAP,
etc) based plots (#127).Split_FeatureScatter
function has been completely deprecated and it’s functionality has been
moved to new FeatureScatter_scCustom.gene_list in Iterate_FeaturePlot_scCustom and
Iterate_VlnPlot_scCustom has been soft-deprecated and
replaced by features parameter. Specifying
gene_list will display deprecation warning but continue to
function until next major update.Read10X_Metrics to use new internal
helper functions.Liger_to_Seurat to transfer the liger_object@H
slot in addition to H.norm slot already moved.length(x = colnames(x = obj) with
length(x = Cells(x = obj) for accurate plotting based on V5
object structure.Gene_Present now accepts assay
parameter.R/ for
better organization.scCustomize_Palette). Now if number of colors is greater
than 2 but less than 8 the default palette will be
ColorBlind_Pal (previously it was “polychrome”). Polychrome
remains the default when number of colors is between 9-36.scCustomize_Palette to
ggplot_default_colors = FALSE to avoid uncessary error when
no value supplied.DimPlot_scCustom will now set label = TRUE
if label.box is set to TRUE but label is not
changed from default.PackageCheck (now deprecated), with
rlang::is_installed() for non-dependency checks.Read10X_Metrics that caused errors when
reading files on windows operating system (#115).Create_CellBender_Merged_Seurat when
feature names are changed (underscore to dash) during object creation
(#118).Read10X_h5_Mutli_Directory when reading
Cell Ranger multi directories.VlnPlot_scCustom,
DimPlot_scCustom, and DotPlot_scCustom to
avoid otherwise ambiguous error messages (#120).VlnPlot_scCustom (#122).Cell_Highlight_Plot that could
cause function to error without proper error message.Read_* functions to
avoid unnecessary errors.drop_na(.data[[var]], with current dplyr syntax.VlnPlot-based plots when
split.by is not NULL.group.by when using DimPlot_scCustom (#128).Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER
which incorrectly stated the names of new meta.data/cell.data columns to
be added.DotPlot_scCustom that prevented it from
working unless group.by parameter was explicitly
added.Case_Check caused by typo.Cluster_Highlight_Plot
and Meta_Highlight_Plot that were too verbose.Add_Mito_Ribo_Seurat and
Add_Mito_Ribo_LIGER which caused error when supplying
custom list of features for non-default organism (#133).DimPlot_scCustom preventing that errored
when trying to split plot and use figure_plot at same
time.Merge_Seurat_List.aspect_ratio parameter to all dimensionality
reduction plots to control axes ratio of output plot.plot_median and median_size
parameters to QC_Plots_* functions.split_collect parameter to
FeaturePlot_scCustom to collect all guides when using
split.by for a single feature (#94).Clustered_DotPlot to allow
modification of sizes of column text labels, legend text labels, and
legend title labels (#96).Merge_Sparse_Multimodal_All for
merging multi-modal data (1 matrix per modality) (#104).Clustered_DotPlot named
row_label_fontface to allow control of fontface used for
row labels (#103).Reduction_Loading_Present, in part
to fix issue with FeaturePlot_scCustom and internal feature
checking.Clustered_DotPlot using new parameters:
cluster_feature, cluster_ident (#106).dot_size parameter to statistics plotting
functions Plot_Cells_per_Sample and
Plot_Median_* family.no_legend to
Iterate_Meta_Highlight_Plot to allow for plotting with a
plot title instead of plot legend (#108).QC_Plots_Feature to use
VlnPlot_scCustom under the hood like rest of
QC_Plots_* functions.abort in Meta_Present to
return_none to align with Gene_Present and
Reduction_Loading_Present.summarise_at, select(.data[[var]]), and
rename(.data[[var]]) with current dplyr syntax.Iterate_Cluster_Highlight_Plot and
Iterate_Meta_Highlight_Plot to align with recent updates to
base Cluster_Highlight_Plot and
Meta_Highlight_Plot functions.QC_Plots_Feature to respect parameters when
passing to VlnPlot (#91).Read_CellBender_h5_* functions to support
CellBender outputs from STARsolo- or Cell Ranger (pre-V3)-processed data
(#99).FeaturePlot_scCustom to allow for plotting of
dimensionality reduction loadings (#97).Read10X_Multi_Directory and
Read10X_h5_Multi_Directory to support files processed with
Cell Ranger multi pipeline.Merge_Seurat_List that prevented
add.cell.id from adding correct cell name prefixes (#113).label_color_num parameter to
PalettePlot allow control of color labeling.Stacked_VlnPlot 90
degrees or 45 (previously possible) (#84).Merge_Seurat_List to avoid
ambiguous error messages on failure.Case_Check checks/messages to all feature-based
plotting functions.PalettePlot has been changed from palette to
pal.PalettePlot to support pal of
class “colors”.Cluster_Highlight_Plot and
Meta_Highlight_Plot.Fetch_Meta is now S3 generic function that can handle
either Seurat or LIGER objects.R/ scripts for better
organization.Add_Mito_Ribo_Seurat and
Add_Mito_Ribo_LIGER.Add_Mito_Ribo_Seurat to respect provided
mito_name, ribo_name and
mito_ribo_name values.merge parameter to Read10X_GEO,
Read10X_h5_GEO, Read_GEO_Delim and
Read_CellBender_h5_Multi_File.raster.dpi parameter to
DimPlot_LIGER.label parameter to
FeaturePlot_scCustom to avoid error collision (#80).vln_linewidth parameter to control violin outline
line width (#32).Fetch_Meta for
returning data.frame of object meta data.Extract_Sample_Meta to extract sample-level meta
data from object.Cell_Highlight_Plot for highlight plots of custom
cells not in active ident or meta data.flip parameter to Clustered_DotPlot
to enable axes flipping (#69).R/ scripts for better
organization.FindMarkers.CellBender_Feature_Diff to return data.frame with
count sums and differences between raw and CellBender assays.CellBender_Diff_Plot to plot differences between
raw and CellBender assays using data from
CellBender_Feature_Diff.Add_CellBender_Diff is new name for
Add_Cell_Bender_Diff in order to unify function names for
CellBender related functions.mito_name parameter to QC_Plots_Mito
to allow for custom specification of meta data column name that contains
mitochondrial information.QC_Plots_Combined_Vln() function to return
patchwork layout of 3 QC plots.Add_Mito_Ribo_Seurat() and
Add_Mito_Ribo_LIGER() (#28).alpha_exp and alpha_na_exp
parameters to FeaturePlot_scCustom to allow for control of
color scale transparency (#21).*_Highlight_Plot functions can now plot multiple
variables simultaneously using either one color for all variables or one
color per variable (#34).figure_plot to
DimPlot_scCustom(). This removes axes and axes labels and
adds axis legend on left bottom corner of plot (#40).plot_legend to
Stacked_VlnPlot. This solves issue with returning only one
shared legend across all features being plotted (#48).Add_Cell_Complexity_Seurat and
Add_Cell_Complexity_LIGER functions to add cell QC
complexity/novelty metric (log10(Genes) / log10(UMIs)).QC_Plots_Complexity plot for quick plotting of
cell complexity score.Read_CellBender_h5_Mat,
Read_CellBender_h5_Multi_Directory,
Read_CellBender_h5_Multi_File to enable easy reading of new
CellBender output files.raster.dpi parameter from Seurat to all
DimPlot FeaturePlot or
FeatureScatter based functions.add.noise parameter from Seurat to
VlnPlot_scCustom Stacked_VlnPlot
functions.group.by as default listed parameter to added to
allVlnPlot based QC_Plot_*.ensembl_ids parameter for
Add_Mito_Ribo_* functions. If
ensembl_ids = TRUE functions will retrieve stored ensembl
IDs representing mitochondrial and ribosomal genes for accepted default
species.label_feature_yaxis to
FeaturePlot_scCustom. Allows for plotting of feature names
on secondary y-axis when using split.by (#60).Add_Sample_Meta function for addition of
sample-level meta data to cell-level @meta.data slot of
Seurat objects.Read_GEO_Delim to check for
issues with imported matrices. Check is modified version of
SeuratObject::CheckMatrix called
CheckMatrix_scCustom(). Will warn if infinite, logical,
non-integer (whole), or NA/NaN values are detected in input
matrix.QC_Plot_UMIvsGene will now returned filtered
correlation value that takes into account
meta_gradient_name if provided in addition to nFeature_RNA
and nCount_RNA.Variable_Features_ALL_LIGER which
allows for detection/selection of variable genes from entire LIGER
object instead of iterating by dataset.PackageCheck warning has been added where needed.VlnPlot has been changed to
Iterate_VlnPlot_scCustom to reflect that it now uses
VlnPlot_scCustom to generate plots.QC_Plot_* functions now use
VlnPlot_scCustom internally to unify color scheme and
rasterization parameters.*_Highlight_Plot functions no longer display
“Unselected” in plot legend and uses DimPlot_scCustom to
generate plots (#34).low_cutoff from plotting via
QC_Plots_Mito.Clustered_DotPlot that prevented setting
identity colors (#29).FeaturePlot_scCustom that returned NULL
when setting combine = FALSE (#31).Seq_QC_Plot_* functions which resulted in
groups being plotted out of order when specifying plot_by
parameter.Seq_QC_Plot_* functions that created color
palette error when color palettes were not being used.DimPlot_scCustom that caused mismatch of
colors between plots when using split.by if one of the
plots was missing 1 or more of the group.by levels (#37).VlnPlot_scCustom that caused raster
warning messages to be displayed twice (#42).Iterate_PC_Loading_Plots that caused error
when specifying current directory with file_path = NULL or
file_path = ""DotPlot_scCustom that prevented plotting
of features in meta.data slot (#44).Stacked_VlnPlot when
no supplied features were present.plotFactors_scCustom that was ignoring
provided file name.plotFactors_scCustom that caused progress
to only display progress up to 50% even when it was fully complete.Clustered_DotPlot that resulted in error
related to color palettes if number of clusters was greater than 36 (#49).Add_Mito_Ribo_LIGER that resulted custom
column names (e.g. mito_name = "pct.mt") being disregarded
and also therefore issue with overwrite parameter. (#51).Store_Misc_Info_Seurat that prevented
function from working.Plot_Density_Custom when supplying
custom_palette and multiple features. (#51).Clustered_DotPlot so that legend with
identities is displayed by factor level of Seurat object idents (#55).Split_FeatureScatter to remove test code
that prevented function from working properly (#57).DimPlot_All_Samples,
Split_FeatureScatter, and DimPlot_scCustom
that ignored factor order when plotting groups.FeaturePlot_scCustom
when setting split.by and one or more of features provided
was not present in object (#64).VlnPlot_scCustom function.Stacked_VlnPlotmake_unique parameter to
Extract_Top_Markers function.Clustered_DotPlot function.Add_Mito_Ribo_Seurat and
Add_Mito_Ribo_LIGER.VlnPlot.Read_Metrics_10X errors that occurred due to
differing outputs depending on Cell Ranger version or type of
assay.importFrom for
DefaultDimReduc from SeuratObject package to avoid
potential errors.Read_Metrics_10X errors that occurred due to
differing outputs depending on Cell Ranger version or type of
assay.importFrom for
DefaultDimReduc from SeuratObject to avoid potential
errors.Merge_Sparse_Data_All. (#8)Read_Metrics_10X,
Read10X_Multi_Directory, and
Read10X_h5_Multi_Directory.StackedVlnPlot with
parameters plot_spacing and spacing_unit. (#6)scCustomize_Palette function select palette to
use (simplify internal code).Iterate_VlnPlot.Iterate_... function checks for file path parameter
if file_path = NULL.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.