Introduction | Mini overview of magmaR, magma, and the UCSF Data Library system | Scope of this vignette | How magmaR functions work | Upload Functions | Overview | Common features | Running non-interactively | Example Data | Function Details | updateMatrix() | Necessary inputs: | updateFromDF() | updateValues() | Session information

Quick Start | Introduction | magmaR, magma, and the UCSF Data Library | Organization of data within magma | How magmaR functions work | Data Restructuring Details | The two main output structures of magma returns | Installation | Authorization process, a.k.a. janus token utilization: | Providing a token | When magma thinks you are unauthorized | Controlling which version of magma to target | Helper functions | Main data download functions: | retrieve() & retrieveJSON() | retrieveMatrix() | query() | retrieveMetadata() | Putting it all together | Session information

Introduction | Color-blindness friendliness: | Disclaimer | Installation | Quick-Reference: Seurat<=>dittoSeq | Functions | Inputs | Setup: Some simple preprocessing | Getting started | Single-cell RNAseq data | Bulk RNAseq data | Additional details on bulk data import: | Helper Functions | Metadata | Genes/Features | Reductions | Characteristic: Bulk versus single-cell | Visualizations | dittoDimPlot & dittoScatterPlot | Additional features | dittoDimHex & dittoScatterHex | Summary function control | dittoPlot (and dittoRidgePlot + dittoBoxPlot wrappers) | Adjustments to data representations | dittoBarPlot & dittoFreqPlot | dittoHeatmap | Multi-Plotters | dittoDotPlot | multi_dittoPlot & dittoPlotVarsAcrossGroups | multi_dittoDimPlot & multi_dittoDimPlotVaryCells | Customization via Simple Inputs | Subsetting to certain cells/samples | Faceting with split.by | All titles are adjustable. | Colors can be adjusted easily. | Underlying data can be output. | plotly hovering can be added. | Rasterization / flattening to pixels | Session information | References