Package index • Luciernaga

All functions

AveragedSignature(): Summarize a data.frame to desired stat

Luciernaga_Brightness(): Visualize MFI of raw .fcs files to evaluate single color controls.

Luciernaga_FCSToReport(): Visualize cosine similarity of raw .fcs files to evaluate single color controls.

Luciernaga_IterativeUnmixing(): Iterates over single color variant .fcs files, passing the generated signature to unmix full-stain sample

Luciernaga_LinearSlices(): Takes a Lucierna SingleColorQC .fcs, splits into percentiles, and plots the results.

Luciernaga_Lists(): Generate Luciernaga plot outputs from List of List

Luciernaga_Move(): Transfer the .fcs files selected by LuciernagaTree to a new location

Luciernaga_Plots(): Converts the Luciernaga outputs into .pdf plots

Luciernaga_QC(): Main Luciernaga Function, normalized on individual cell level

Luciernaga_SingleColors(): Calculates the single color control matrix for a given quantile cutoffs and a given statistic

Luciernaga_Tree(): Select candidate Luciernaga output .fcs files for future use in unmixing.

Luciernaga_Unmix(): OLS unmixing of a Gating Set object

NameCleanUp(): Shorten a variable name

QC_FilePrep(): Converts the Cytek Aurora (TM)'s QC report into a data frame.

QC_GainMonitoring(): Takes Before After QC .fcs files of QC beads run on assay settings, returns the gains and average measurement in a data.frame to allow for plotting to assess stability over time.

QC_LibraryParse(): Parses Library Reference Control .XML files and returns

QC_Plots(): Takes the dataframe generated from CytekQCFilePrep and returns all the QC plots

QC_ProspectiveAdditions(): From existing panel, figures out open detectors, and returns potential fluorophores that might fit between the existing ones

QC_ReferenceLibrary(): Queries the available reference library for available fluorophores (and their naming conventions)

QC_Retrieval(): Returns Detector Gains, Laser Delay and Scalings from individual .fcs files in a CytoSet.

QC_SimilarFluorophores(): Queries fluorophore and returns similar fluorophores.

QC_UserLibraries(): Takes data.frame of QC_LibraryParse, and iterating over individual users returns plots

QC_ViewSignature(): Visualizes the Signature for given row in an averaged signature data.frame.

QC_WhatsThis(): Querries reference signatures and returns most similar fluorophores by cosine similarity.

Utility_ColAppend(): Add Dimensionality Visualized parameters to raw .fcs files

Utility_Concatinate(): Concatenate a gs based on subset and optional subsample

Utility_DensityOverlay(): Generates an overlay plot containing all objects in the GatingSet

Utility_Downsample(): Downsample a gs based on subset

Utility_GatingPlots(): Check gate placement for individual .fcs files in a GatingSet

Utility_IterativeGating(): Return individual plots for specified node for specimens within a GatingSet.

Utility_NbyNPlots(): Generate NxN plots for one or all fluorophores.

Utility_PaCMAP(): Runs PaCMAP via Basilisk

Utility_ParallelNbyNPlots(): Overlay plot two .fcs files from two different gs.

Utility_Patchwork(): Generate the plots into a single pdf

Utility_Phate(): Runs PHATE via Basilisk

Utility_RidgePlots(): Draw Ridge Plots for comparison

Utility_ThirdColorPlots(): Highlight the location of a particular cell population on a given bi-exponential axis.

Utility_tSNE(): Runs tSNE (Rtsne implementation)

Utility_UMAP(): Runs UMAP (uwot implementation)

Utility_UnityPlot(): Compare the plots for given parameters for all specimens in the gating set.

Wetlab_Concentration(): Takes gated .fcs files and returns concentration and other info useful for Wetlab users.

Wetlab_Decision(): Takes Rest output, and referencing TheCondition csv makes decision for culture resuspensions

Wetlab_Rest(): Takes Concentration output, returns re-suspension amounts for Wetlab users.