Gates/filters in Flow Cytometry Data Visualization | abstract | Introduction | Filters and filter results | Visualization | Example Data | Filters in scatter plots | Simple Geometric Filter Types | Data-Driven Filters | Filters in one-dimensional density plots | Plotting parameters | Restrictions on the formula interface | Filters in parallel coodinate plots

1.1. Manual gating | 1.2. Automated Gating | 2.1. Template format | 2.2. Example template | 2.2.1. "nonDebris" | 2.2.2. "singlets" | 2.2.3. "lymphocytes" | 2.2.4. "cd3+" (Tcells) | 2.2.5. CD4 and CD8 | 4.1. Load the raw data | 4.2. Compensation | 4.3. Transformation | 4.5. Gating | 4.6. Hide nodes | 4.7. Rename nodes | 4.8. Visualize the gates | 4.9. Apply a gating method without csv template

1D gating methods | mindensity | tailgate | quantileGate | 2D gating methods | boundary Gate | singletGate | flowClust.2d | Transitional gate | quadGate.tmix

pop = "+/-" | pop = "++" | pop = "+/-+/-" | Gating method that generates multiple populations | pop = "*" and alias = "A,B,C" | pop = "" and alias = "" | Single row with multiple parents (i.e. parent ="A,B,C")

Automated gating | Load raw FCS files into GatingSet | Compensate and transform | Load the gating template and run auto gating | Export to Cytobank | Export to FlowJo

1: support 3 types of plot constructor | low level: ggplot | GatingSet | flowSet/ncdfFlowSet/flowFrame | gates | medium level: ggcyto | top level: autoplot | 2: in-line transformation | 3: generic geom_gate layer | 4: geom_stats | 5: axis_inverse_trans | 6: auto limits | 7: labs_cyto | 8: ggcyto_par_set | 9: as.ggplot | 10: ggcyto_layout

Introduction | Representing Flow Cytometry Data | Reading and Manipulating flowCore Data Classes | Visualizing Flow Cytometry Data | Compensation | Transformation | Gating | Extensions from flowWorkspace: GatingHierarchy and GatingSet

Basics | open the workspace | Extract groups from xml | Extract Samples from xml | Extract keywords from xml | Parse with default settings | select group | FCS path | string | data.frame | Advanced | Parsing xml without loading FCS | Additional keys to tag samples | additional.keys | additional.sampleID | Annotate sample with keywords | keywords | keywords.source | keyword.ignore.case | Import a subset | Parallel parsing | Skip leaf boolean gates | Skip faulty gates | Import the empty gating tree | Customized fcs file extension

Representing Flow Cytometry Data with ncdfFlowSet | Creating a ncdfFlowSet | Working with metadata | Manipulating a ncdfFlowSet | Compensation,Transformation and Gating | Subsetting

1d histogram/densityplot | stacked density plot | 2d scatter/dot plot | Add geom_gate and geom_stats layers

flowSet | flowFrame | GatingSet | GatingHierarchy | ggcyto_arrange

ggcyto_par_set | geom_gate | geom_stats | geom_overlay | subset | axis_x_inverse_trans