### Install SCpubr from GitHub Source: https://github.com/enblacar/scpubr/blob/main/README.md Installs the latest stable development version of the SCpubr package from GitHub using the devtools package. Ensure devtools is installed first if necessary. ```r if(!requireNamespace("devtools", quietly = TRUE)){ install.packages("devtools") # If not installed. } devtools::install_github("enblacar/SCpubr", ref = "v2.0.0-dev-stable") ``` -------------------------------- ### Install SCpubr from CRAN Source: https://github.com/enblacar/scpubr/blob/main/README.md Installs the official release version of the SCpubr package from CRAN. ```r install.packages("SCpubr") ``` -------------------------------- ### GPL Notice for Terminal Interaction Source: https://github.com/enblacar/scpubr/blob/main/LICENSE.md Display this notice when a program starts in interactive mode to inform users about its free software status and warranty limitations. ```text Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details. ``` -------------------------------- ### Standard GPL Notice for Source Files Source: https://github.com/enblacar/scpubr/blob/main/LICENSE.md Include this notice at the beginning of each source file to clearly state the program's name, copyright, and licensing terms under the GNU GPL. ```text Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . ``` -------------------------------- ### Generate Package Report Source: https://github.com/enblacar/scpubr/blob/main/README.md Generates a comprehensive report detailing missing dependencies and available functions for SCpubr. Set extended to TRUE for a more detailed report. ```r SCpubr::package_report(extended = TRUE) ``` -------------------------------- ### SCpubr::do_ExpressionHeatmap Source: https://github.com/enblacar/scpubr/blob/main/NEWS.md Adds parameters for clustering and custom ordering to the ExpressionHeatmap function, allowing for more control over the heatmap visualization. ```APIDOC ## SCpubr::do_ExpressionHeatmap ### Description Adds parameters for clustering and custom ordering to the ExpressionHeatmap function, allowing for more control over the heatmap visualization. ### Parameters - `cluster` (boolean) - Allows for clustering of rows and columns. - `groups.order` (list) - Allows for specifically arranging the groups defined by `group.by` with a given order. - `features.order` (list) - Allows for specifically arranging the features defined by `features`. ``` -------------------------------- ### SCpubr::do_FeaturePlot Source: https://github.com/enblacar/scpubr/blob/main/NEWS.md Introduces several new parameters to FeaturePlot for enhanced cell highlighting, group visualization, and border control. It also renames `split.by.idents` for better synergy with `do_DimPlot`. ```APIDOC ## SCpubr::do_FeaturePlot ### Description Introduces several new parameters to FeaturePlot for enhanced cell highlighting, group visualization, and border control. It also renames `split.by.idents` for better synergy with `do_DimPlot`. ### Parameters - `border.density` (numeric) - Controls the density of background points for cell borders (0-1). - `group.by` (string) - Plots a large dot in the center of each group to aid location. - `group.by.show.dots` (boolean) - Controls whether group dots are plotted. - `group.by.dot.size` (numeric) - Controls the size of the group dots. - `group.by.cell_border` (boolean) - Plots a contour-like border around cells indicating cluster reach. - `group.by.cell_borders.alpha` (numeric) - Controls the alpha of the new cell borders. - `group.by.legend` (string) - Controls the legend title for group information. - `idents.keep` (string) - Renamed from `split.by.idents`, works with `split.by`. ### Changes - Modified underlying code to show a border around selected cells when using `split.by`, `cells.hightlight`, and `idents.highlight`. ``` -------------------------------- ### SCpubr::do_DotPlot Source: https://github.com/enblacar/scpubr/blob/main/NEWS.md Enhances the DotPlot function with a new `scale` parameter and improved handling of `flip` and `features`. The `split.by` parameter has been removed for better consistency. ```APIDOC ## SCpubr::do_DotPlot ### Description Enhances the DotPlot function with a new `scale` parameter and improved handling of `flip` and `features`. The `split.by` parameter has been removed for better consistency. ### Parameters - `scale` (boolean) - Allows for the data to be scaled or not scaled. - `cluster` (alias for `cluster.idents`) - Allows for clustering of idents. ### Changes - Removed `split.by` parameter. - Renamed parameter `cluster.idents` to `cluster`. - Removed the limitation of `flip` when `features` was a list of genes, allowing any combination. ``` -------------------------------- ### SCpubr::do_EnrichmentHeatmap Source: https://github.com/enblacar/scpubr/blob/main/NEWS.md Updates the EnrichmentHeatmap function to simplify plotting options and enforce structured input. It now allows clustering and custom ordering of groups and features. ```APIDOC ## SCpubr::do_EnrichmentHeatmap ### Description Updates the EnrichmentHeatmap function to simplify plotting options and enforce structured input. It now allows clustering and custom ordering of groups and features. ### Parameters - `return_object` (boolean) - Returns the Seurat object with enrichment scores as a new Assay. - `cluster` (boolean) - Allows for clustering of rows and columns. - `groups.order` (list) - Allows for specifically arranging the groups defined by `group.by` with a given order. - `features.order` (list) - Allows for specifically arranging the gene sets defined by `input_gene_list`. ### Changes - Removed options for plotting FeaturePlots, GeyserPlots, ViolinPlots, etc. - Removed `return_matrix` parameter; scores are now retrieved from the Seurat object as an assay. - Enforcing the use of `named lists` as input for the function. ``` -------------------------------- ### SCpubr::do_CopyNumberVariantPlot() Source: https://github.com/enblacar/scpubr/blob/main/NEWS.md Generates Copy Number Variant plots. This function has been updated to remove options for Feature and Geyser plots, and now includes a `return_object` parameter to return the Seurat object with CNV scores. The primary output is a heatmap visualizing averaged scores. ```APIDOC ## SCpubr::do_CopyNumberVariantPlot() ### Description Generates Copy Number Variant plots. This function has been updated to remove options for Feature and Geyser plots, and now includes a `return_object` parameter to return the Seurat object with CNV scores. The primary output is a heatmap visualizing averaged scores. ### Parameters - `return_object` (boolean) - Returns the Seurat object with a new assay containing CNV scores. ### Output - Heatmap with averaged CNV scores by chromosome and groups, and by chromosome arms. ``` -------------------------------- ### SCpubr::do_FunctionalAnnotationPlot Source: https://github.com/enblacar/scpubr/blob/main/NEWS.md Streamlines the FunctionalAnnotationPlot by removing tree and bar/dot plot options. It now offers the ability to return the result matrix for further analysis and renames an ordering parameter. ```APIDOC ## SCpubr::do_FunctionalAnnotationPlot ### Description Streamlines the FunctionalAnnotationPlot by removing tree and bar/dot plot options. It now offers the ability to return the result matrix for further analysis and renames an ordering parameter. ### Parameters - `return_matrix` (boolean) - Returns the result matrix for further analysis or visualizations. - `order` (boolean, alias for `order_by_mean`) - Ordering is now based on the median instead of the mean when TRUE. ### Changes - Removed tree plots due to inconsistent behavior and compromised visualization quality. - Removed the option to plot bar plots and dot plots for a simplified generation. - Renamed `order_by_mean` to `order`. ``` -------------------------------- ### SCpubr::do_DimPlot Source: https://github.com/enblacar/scpubr/blob/main/NEWS.md Modifies the display of DimPlots, particularly when highlighting cells or identities. It fixes bugs related to multiple legends and ensures correct border display. ```APIDOC ## SCpubr::do_DimPlot ### Description Modifies the display of DimPlots, particularly when highlighting cells or identities. It fixes bugs related to multiple legends and ensures correct border display. ### Changes - Correctly displays borders around cells when `cells.highlight`, `idents.hightlight`, or `idents.keep` are used. - Removed the redundant "Not selected" item from the legend when highlighting is active. - Fixed a bug causing multiple legends when using `group.by` and `split.by` simultaneously. ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.