aspect_ratioparameter to all dimensionality reduction plots to control axes ratio of output plot.
FeaturePlot_scCustomto collect all guides when using
split.byfor a single feature (#94).
Clustered_DotPlotto allow modification of sizes of column text labels, legend text labels, and legend title labels (#96).
Merge_Sparse_Multimodal_Allfor merging multi-modal data (1 matrix per modality) (#104).
row_label_fontfaceto allow control of fontface used for row labels (#103).
Reduction_Loading_Present, in part to fix issue with
FeaturePlot_scCustomand internal feature checking.
Clustered_DotPlotusing new parameters:
dot_sizeparameter to statistics plotting functions
Iterate_Meta_Highlight_Plotto allow for plotting with a plot title instead of plot legend (#108).
VlnPlot_scCustomunder the hood like rest of
return_noneto align with
rename(.data[[var]])with current dplyr syntax.
Iterate_Meta_Highlight_Plotto align with recent updates to base
QC_Plots_Featureto respect parameters when passing to
Read_CellBender_h5_*functions to support CellBender outputs from STARsolo- or Cell Ranger (pre-V3)-processed data (#99).
FeaturePlot_scCustomto allow for plotting of dimensionality reduction loadings (#97).
Read10X_h5_Multi_Directoryto support files processed with Cell Ranger
add.cell.idfrom adding correct cell name prefixes (#113).
PalettePlotallow control of color labeling.
Stacked_VlnPlot90 degrees or 45 (previously possible) (#84).
Merge_Seurat_Listto avoid ambiguous error messages on failure.
Case_Checkchecks/messages to all feature-based plotting functions.
PalettePlothas been changed from
palof class “colors”.
Fetch_Metais now S3 generic function that can handle either Seurat or LIGER objects.
R/scripts for better organization.
FeaturePlot_scCustomto avoid error collision (#80).
vln_linewidthparameter to control violin outline line width (#32).
Fetch_Metafor returning data.frame of object meta data.
Extract_Sample_Metato extract sample-level meta data from object.
Cell_Highlight_Plotfor highlight plots of custom cells not in active ident or meta data.
Clustered_DotPlotto enable axes flipping (#69).
R/scripts for better organization.
CellBender_Feature_Diffto return data.frame with count sums and differences between raw and CellBender assays.
CellBender_Diff_Plotto plot differences between raw and CellBender assays using data from
Add_CellBender_Diffis new name for
Add_Cell_Bender_Diffin order to unify function names for CellBender related functions.
QC_Plots_Mitoto 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.
FeaturePlot_scCustomto allow for control of color scale transparency (#21).
*_Highlight_Plotfunctions can now plot multiple variables simultaneously using either one color for all variables or one color per variable (#34).
DimPlot_scCustom(). This removes axes and axes labels and adds axis legend on left bottom corner of plot (#40).
Stacked_VlnPlot. This solves issue with returning only one shared legend across all features being plotted (#48).
Add_Cell_Complexity_LIGERfunctions to add cell QC complexity/novelty metric (log10(Genes) / log10(UMIs)).
QC_Plots_Complexityplot for quick plotting of cell complexity score.
Read_CellBender_h5_Multi_Fileto enable easy reading of new CellBender output files.
raster.dpiparameter from Seurat to all
add.noiseparameter from Seurat to
group.byas default listed parameter to added to all
ensembl_ids = TRUEfunctions will retrieve stored ensembl IDs representing mitochondrial and ribosomal genes for accepted default species.
FeaturePlot_scCustom. Allows for plotting of feature names on secondary y-axis when using
Add_Sample_Metafunction for addition of sample-level meta data to cell-level
@meta.dataslot of Seurat objects.
Read_GEO_Delimto check for issues with imported matrices. Check is modified version of
CheckMatrix_scCustom(). Will warn if infinite, logical, non-integer (whole), or NA/NaN values are detected in input matrix.
QC_Plot_UMIvsGenewill now returned filtered correlation value that takes into account
meta_gradient_nameif provided in addition to nFeature_RNA and nCount_RNA.
Variable_Features_ALL_LIGERwhich allows for detection/selection of variable genes from entire LIGER object instead of iterating by dataset.
PackageCheckwarning has been added where needed.
VlnPlothas been changed to
Iterate_VlnPlot_scCustomto reflect that it now uses
VlnPlot_scCustomto generate plots.
QC_Plot_*functions now use
VlnPlot_scCustominternally to unify color scheme and rasterization parameters.
*_Highlight_Plotfunctions no longer display “Unselected” in plot legend and uses
DimPlot_scCustomto generate plots (#34).
low_cutofffrom plotting via
Clustered_DotPlotthat prevented setting identity colors (#29).
FeaturePlot_scCustomthat returned NULL when setting
combine = FALSE(#31).
Seq_QC_Plot_*functions which resulted in groups being plotted out of order when specifying
Seq_QC_Plot_*functions that created color palette error when color palettes were not being used.
DimPlot_scCustomthat caused mismatch of colors between plots when using
split.byif one of the plots was missing 1 or more of the
VlnPlot_scCustomthat caused raster warning messages to be displayed twice (#42).
Iterate_PC_Loading_Plotsthat caused error when specifying current directory with
file_path = NULLor
file_path = ""
DotPlot_scCustomthat prevented plotting of features in meta.data slot (#44).
Stacked_VlnPlotwhen no supplied features were present.
plotFactors_scCustomthat was ignoring provided file name.
plotFactors_scCustomthat caused progress to only display progress up to 50% even when it was fully complete.
Clustered_DotPlotthat resulted in error related to color palettes if number of clusters was greater than 36 (#49).
Add_Mito_Ribo_LIGERthat resulted custom column names (e.g.
mito_name = "pct.mt") being disregarded and also therefore issue with
Store_Misc_Info_Seuratthat prevented function from working.
custom_paletteand multiple features. (#51).
Clustered_DotPlotso that legend with identities is displayed by factor level of Seurat object idents (#55).
Split_FeatureScatterto remove test code that prevented function from working properly (#57).
DimPlot_scCustomthat ignored factor order when plotting groups.
split.byand one or more of features provided was not present in object (#64).
scCustomize_Palettefunction select palette to use (simplify internal code).