News
Here are the patch notes of the different versions:
SCpubr v1.1.1.9000
Current development release.
SCpubr v1.1.1
Hotfixes in unit tests to comply with CRAN checks.
SCpubr v1.1.0
General
- Increased the cell size of all heatmap-based functions from 5 to 8.
- Decreased the thickness of frame and ticks of all ggplot2-based continuous legends to retrieve a similar behavior as in previous versions of ggplot2, as with the new update, the overall thickness of the frame and ticks increased, probably due to the changes related to
element_line
, - Added five new functions:
do_AlluvialPlot()
,do_AzimuthAnalysisPlot()
,do_ExpressionHeatmap()
,do_GroupedGOTermPlot()
anddo_FunctionalAnnotationPlot()
. - Added
legend.ncol
,legend.nrow
,legend.title
andlegend.byrow
to as many functions as possible to further customize legend appearance.
SCpubr::do_BeeSwarmPlot()
- Added
min.cutoff
andmax.cutoff
parameter. - Added ticks to the plot, that were missing.
- Added missing axes titles.
- Added
viridis_direction
parameter to control how the continuous color scale is formed. - Added
return_object
parameter to return the Seurat object with the enrichment scores computed. - Added BoxPlots, BeeSwarmPlots and ViolinPlots to the possible outputs the user can choose from.
- Make
legend.position
conditional of whethercontinuous_feature
is set to TRUE. If it is false, legend is not displayed unless the user specifies otherwise.
SCpubr::do_BarPlot()
- Fixed a bug in which axes titles were not displaying correctly under certain combinations of
flip
andsplit.by
. - Fixed a bug in which
x_lab
andy_lab
would not rotate accordingly when usingflip = TRUE
.
SCpubr::do_BoxPlot()
- Set
assay
to NULL and will default to the default assay in the seurat object.
SCpubr::do_CellularStatesPlot()
- Fixed a bug that prevented FeaturePlots to have symmetrical axes with respect to the main plot.
SCpubr::do_CorrelationPlot()
- Added
viridis_direction
parameter.
SCpubr::do_DimPlot()
- Fixed a bug in which the legend title will not show up in regular basic plots even though the parameter
legend.title
was used. - Completely reformatted the way
split.by
works, so that now only one legend is displayed for the whole group and cells have border. - Added
label.size
andlabel.box
parameters for further customize the appearance of the plot when usinglabel = TRUE
. - Changed
repel
toFALSE
by default.
SCpubr::do_EnrichmentHeatmap()
- Fixed a bug in the code that prevented the feature plots and the geyser plots to be computed if the input gene list was not a named list of genes.
- Added
flavor = "AUCell"
, that lets the user compute AUCell scoring of the gene sets. - Added the option to query multiple
group.by
parameters at the same time. - Fixed a bug in the code that prevented multiple outputs with different values of
group.by
to be returned properly, leading to the last value ofgroup.by
replacing all the rest.
SCpubr::do_FeaturePlot()
- Added
label
,label.size
andlabel.color
parameter to reproduce the same behavior as inSeurat::FeaturePlot()
.
SCpubr::do_GroupwiseDEPlot()
- Set
assay
to NULL and will default to the default assay in the seurat object.
SCpubr::do_LigandReceptorPlot()
- Added
arrange_interactions_by
to control how output interactions are arranged (either by aggregate_rank, specificity, magnitude or a combination of magnitude and specificity). - Added
sort_interactions_alphabetically
to control whether the output dotplot has the interactions ordered alphabetically or as they come in the original matrix (meaning, they follow the arrangement specified inarrange_interactions_by
). ((liana’s issue #72))
do_PathwayActivityPlot()
- Added a fix in which when
enforce_symmetry
is set toFALSE
, then the color scale turns into a viridis-based one instead of a two-color gradient scale.
do_TFActivityPlot()
- Added a fix in which when
enforce_symmetry
is set toFALSE
, then the color scale turns into a viridis-based one instead of a two-color gradient scale.
SCpubr::do_ViolinPlot()
- Fixed a bug in the code in which no different colors could be passed to
colors.use
. - Reduced default line width from 1 to 0.5.
SCpubr v1.0.4
- Hotfix for v1.0.3 in which
do_GeyserPlot
with categorical variables had a bug that mapped the legend to the continuous axis.
SCpubr v1.0.3
General changes
- Added
min.cutoff
andmax.cutoff
parameter to effectively subset the color scale and remove the effect of extreme outliers in all ComplexHeatmap-based functions. - Added
min.cutoff
andmax.cutoff
parameter to effectively subset the color scale and remove the effect of extreme outliers in all ggplot2-based functions susceptible to be biased by outliers.
SCpubr::do_DimPlot()
- Implemented a change in which when using
split.by
andgroup.by
in combination, the cells colored on top of the UMAP also have a border. - Implemented a bug-fix in which when using
split.by
andgroup.by
in combination, the extra new layers would not raster ifraster = TRUE
. - Implemented a bug-fix in which when using
split.by
andgroup.by
in combination, no plots will appear ifncol
is set. - Implemented a new feature to add density line contours using
plot_density_contour
. - Implemented the conditional use of
raster.dpi
to Seurat versions higher or equal to 4.1.0.
SCpubr::do_EnrichmentHeatmap()
- Implemented a bug fix for internal checks in the function.
- Added
plot_FeaturePlots
andplot_GeyserPlots
to also report the enrichment scores in a gene set-based manner. - Added
flavor
parameter, that acceptsSeurat
andUCell
to allow for different enrichment scoring methods. It requiresR 4.2.0
to run. - Renamed
symmetrical_scale
toenforce_symmetry
to have a greater coherence accross functions.
SCpubr::do_FeaturePlot()
- Implemented a new feature to add density line contours using
plot_density_contour
. - Implemented the conditional use of
raster.dpi
to Seurat versions higher or equal to 4.1.0.
SCpubr::do_GeyserPlot()
- Fixed bug in which internal parameter names made it to the X axis title.
- Removed
color.by
implementation due to it being very buggy. This will be re-implemented in a future patch.
SCpubr::do_RidgePlot()
- Implemented a bug-fix in which using
assay = "RNA"
or, in fact, any other assay rather thanSCT
will result in an error.
SCpubr::do_ViolinPlot()
- Corrected a bug in which legend title when using
split.by
was an actual line of code. - Added
legend.title
parameter to control the title of the legend.
This version can be obtained in the v1.0.3 release release or downloading it from CRAN using:
SCpubr v.1.0.3-dev-stable
- Same as v1.0.3, but with all the functions that do not pass CRAN checks. These functions are:
SCpubr::save_Plot()
SCpubr::do_LigandReceptorPlot()
andSCpubr::do_SankeyPlot()
.
This version can be obtained in the v1.0.3-dev-stable release release.
SCpubr v1.0.2
General changes
- Change color palette when using
enforce_symmetry = TRUE
to have the middle color asgrey95
instead of the previous one, which made middle values seem closer to the positive end of the scale. - Modified internal structure of all functions to abide with tidyselect v1.2.0 lifecycle modifications.
- Modified
rotate_x_axis_labels
parameter in all functions that made use of it. Now, instead of accepting alogical
, accepts anumeric
: either0
,45
or90
, corresponding to the degrees in which the X axis labels should be rotated. (#5)
SCpubr::do_CopyNumberVariantPlot
- Modified the code for
SCpubr::do_CopyNumberVariantPlot
to also report results for the whole chromosome as well as for each chromosome arm. - Include the
verbose
argument toSCpubr::do_CopyNumberVariantPlot
to silence the messages when there are not enough genes in the chromosome to perform the analysis.
SCpubr::do_DimPlot()
- Fixed a typo that prevented labels to be bold in
SCpubr::do_DimPlot()
when cell borders are displayed. - Added
group.by
andsplit.by
functionality toSCpubr::do_DimPlot()
. (#4)
SCpubr::do_DotPlot()
- Added ticks to axes.
- Modified default colors to convey a better aesthetic.
SCpubr::do_FeaturePlot()
- Fixed potential bugs in
SCpubr::do_FeaturePlot
when settingenforce_symmetry = TRUE
. - Changed default value of
order
inSCpubr::do_FeaturePlot()
fromTRUE
toFALSE
. - Added
min.cutoff
andmax.cutoff
parameters toSCpubr::do_FeaturePlot()
. This allows to effectively subset the color scale to the values provided. Cells outside the range will be converted to the min or max values provided, respectively. (#2)
SCpubr::do_GeyserPlot()
- Added
flip
parameter.
SCpubr::do_GroupwiseDEPlot()
SCpubr::do_LigandReceptorPlot()
(development release)
- Changed parameter
x_labels_angle
torotate_x_axis_labels
to keep a consistent terminology.
SCpubr::do_RidgePlot()
- Fixed a typo that made the lines in
panel.grid.minor
to be displayed inSCpubr::do_Ridgeplot()
. - Added
flip
parameter.
SCpubr::do_ViolinPlot()
- Added
split.by
functionality toSCpubr::do_ViolinPlot()
. (#4, #5) - Added
flip
parameter. - Now multiple features can be queried ad the same time. (#5)
- Changed
feature
parameter tofeatures
, to better reflect the multiple feature behavior. - Recreated
Seurat
’sshare.y.lims
behavior and set it toshare.y.lims
parameter. (#5)
SCpubr v1.0.2-dev-stable
- Same as v1.0.2, but with all the functions that do not pass CRAN checks. These functions are:
SCpubr::save_Plot()
SCpubr::do_LigandReceptorPlot()
andSCpubr::do_SankeyPlot()
.
This version can be obtained in the v1.0.2-dev-stable release release.
SCpubr v1.0.1
- Rework on unit tests and examples so that it can pass CRAN R CMD Check without packages in Suggests. This is, to make sure all Suggested packages are used conditionally.
SCpubr v1.0.1-dev-stable
- Same as v1.0.1, but with all the functions that do not pass CRAN checks. These functions are:
SCpubr::save_Plot()
SCpubr::do_LigandReceptorPlot()
andSCpubr::do_SankeyPlot()
.
This version can be obtained in the v1.0.1-dev-stable release release.
SCpubr v1.0.0
- Modified internal checks so that the functions that do not use
Seurat
do not require this to be installed. This is just for the very side case in which somebody downloads the package just for theSCpubr::do_ColorPalette()
function. - Removed the option to use
individual.titles
, ’individual.subtitlesand
individual.captionsin
SCpubr::do_NebulosaPlot()` as the benefit of such parameters did not surpass the problems the code was causing. The feature might come back in the future, once fully optimized. - Removed
SCpubr::save_Plot()
function to align with CRAN policies that the package should not write to the file system. The code is still available in the v0.0.0.0.9000 release in Github. - Removed
SCpubr::do_LigandReceptorPlot()
,SCpubr::do_SankeyPlot()
andSCpubr::do_PseudotimePlot()
to align with CRAN policies and make it possible to publish the package. These functions can still be accessed in the v0.0.0.0.9000 release in Github. - Removed
SCpubr::do_PseudotimePlot()
for the reason above and because the dependencyMatrix.utils
was removed from CRAN on 09-10-2022.
This version can be obtained in the v1.0.0 release release.
SCpubr v1.0.0-dev-stable
- Same as v1.0.0, but with all the functions that do not pass CRAN checks. These functions are:
SCpubr::save_Plot()
SCpubr::do_LigandReceptorPlot()
andSCpubr::do_SankeyPlot()
.
This version can be obtained in the v1.0.0-dev-stable release release.
SCpubr 0.0.0.9000
- Added a
NEWS.md
file to track changes to the package. - Prepare package for submission to CRAN.