NEWS.md
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.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).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
.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_VlnPlot
make_unique
parameter to Extract_Top_Markers
function.Clustered_DotPlot
function.Add_Mito_Ribo_Seurat
and Add_Mito_Ribo_LIGER
.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).