Package index • Luciernaga

All functions

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

CytosetScreen(): Checks and filters .fcs files into compatible sublist to pass on to CytoSet without crashing out due to mismatch

HolisticToArchived(): Converts the extracted BeadData into the ArchivedData format needed to plot Gain/RCV fails

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

Luciernaga_BrigtnessOverTime(): Visualizes Cluster MFI over time, uses Luciernaga_QC output

Luciernaga_Cosine(): Generates cosine comparison from a data.frame of fluorescent signatures

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

Luciernaga_FolderBrightness(): Sister function to FolderSignature, returns a density plot of brightness

Luciernaga_FolderSignatures(): Takes a folder of Luciernaga_QC signatures and returns a data.frame of the signatures contained within, for use in downstream data analysis.

Luciernaga_GroupHeatmap(): A group version of the heatmap option from Luciernaga_Plots

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_SignatureExternalUnstained(): Wrapper for LuciernagaQC for large scale profiling. Matches unstained with single colors for respective dates, extracts signature and plots, returns data.frame and list of patchwork objects.

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

MarginClean(): Adds openCyto boundary gates at designated location, selectively cleaning out margin events that mess with various algorithms. Can return template for redo editing, as well as returns plots for troubleshooting.

NameCleanUp(): Shorten a variable name

QC_Amalgamate(): Taking a Luciernaga_Slices (or similar data.frame) with an added Counts column, expands each row by the count, takes the median, and then returns either data or a plot showing how different the average signature is from the individual ones

QC_FilePrep_DailyQC(): Converts Cytek Aurora Daily QC report into a data frame.

QC_FilePrep_LJTracking(): 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.

RCVfromFCS(): Calculate the RCV value for each marker for a specified GatingSet subset

TransformationCheck(): Check the transformation settings to visualize .fcs files

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

Utility_Patchwork(): Generate the plots into a single pdf

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.