Contents

1 Data examples

2 Normalization

CATALYST provides an implementation of bead-based normalization as described by Finck et al. (1). Here, identification of bead-singlets (used for normalization), as well as of bead-bead and cell-bead doublets (to be removed) is automated as follows:

  1. beads are identified as events with their top signals in the bead channels
  2. cell-bead doublets are remove by applying a separation cutoff to the distance between the lowest bead and highest non-bead signal
  3. events passing all vertical gates defined by the lower bounds of bead signals are removed (these include bead-bead and bead-cell doublets)
  4. bead-bead doublets are removed by applying a default \(median\;\pm5\;mad\) rule to events identified in step 2. The remaining bead events are used for normalization.

2.1 Normalization work-flow

2.1.1 concatFCS: Concatination of FCS files

Multiple flowFrames or FCS files can be concatenated via concatFCS, which takes either a flowSet, a list of flowFrames, a character specifying the location of the FCS files to be concatinated, or a vector of FCS file names as input. If out_path=NULL (the default), the function will return a single flowFrame containing the measurement data of all files. Otherwise, an FCS 3.0 standard file of the concatenated data will be written to the specified location.

library(CATALYST)
data(raw_data)
ff <- concatFCS(raw_data)

2.1.2 normCytof: Normalization using bead standards

Since bead gating is automated here, normalization comes down to a single function that takes a flowFrame as input and only requires specification of the beads to be used for normalization. Valid options are:

  • "dvs" for bead masses 140, 151, 153, 165, 175
  • "beta" for bead masses 139, 141, 159, 169, 175
  • or a custom numeric vector of bead masses

By default, we apply a \(median\;\pm5\;mad\) rule to remove low- and high-signal events from the bead population used for estimating normalization factors. The extent to which bead populations are trimmed can be adjusted via trim. The population will become increasingly narrow and bead-bead doublets will be exluded as the trim value decreases. Notably, slight over-trimming will not affect normalization. It is therefore recommended to choose a trim value that is small enough to assure removal of doublets at the cost of a small bead population to normalize to.

normCytof(x=ff, y="dvs", k=300)
## Identifying beads...
## Computing normalization factors...

## A flowSet with 2 experiments.
## 
##   column names:
##   Time La139Di Ce140Di Pr141Di Nd142Di Nd143Di Nd144Di Nd145Di Nd146Di Sm147Di Nd148Di Sm149Di Nd150Di Eu151Di Sm152Di Eu153Di Sm154Di Gd155Di Gd156Di Gd158Di Tb159Di Gd160Di Dy161Di Dy162Di Dy163Di Dy164Di Ho165Di Er166Di Er167Di Er168Di Tm169Di Er170Di Yb171Di Yb172Di Yb173Di Yb174Di Lu175Di Yb176Di Ir191Di Ir193Di

3 Debarcoding

CATALYST provides an implementation of the single-cell deconvolution algorithm described by Zunder et al. (2). The package contains three functions for debarcoding and three visualizations that guide selection of thresholds and give a sense of barcode assignment quality.

In summary, events are assigned to a sample when i) their positive and negative barcode populations are separated by a distance larger than a threshold value and ii) the combination of their positive barcode channels appears in the barcoding scheme. Depending on the supplied scheme, there are two possible ways of arriving at preliminary event assignments:

  1. Doublet-filtering:
    Given a binary barcoding scheme with a coherent number \(k\) of positive channels for all IDs, the \(k\) highest channels are considered positive and \(n-k\) channels negative. Separation of positive and negative events equates to the difference between the \(k\)th highest and \((n-k)\)th lowest intensity value. If a numeric vector of masses is supplied, the barcoding scheme will be an identity matrix; the most intense channel is considered positive and its respective mass assigned as ID.
  2. Non-constant number of 1’s:
    Given a non-uniform number of 1’s in the binary codes, the highest separation between consecutive barcodes is looked at. In both, the doublet-filtering and the latter case, each event is assigned a binary code that, if matched with a code in the barcoding scheme supplied, dictates which row name will be assigned as ID. Cells whose positive barcodes are still very low or whose binary pattern of positive and negative barcodes doesn’t occur in the barcoding scheme will be given ID 0 for “unassigned”.

All data required for debarcoding are held in objects of class dbFrame (see Appendix), allowing for the following easy-to-use work-flow:

  1. as the initial step of single-cell deconcolution, assignPrelim will return a dbFrame containing the input measurement data, barcoding scheme, and preliminary event assignments.
  2. assignments will be made final by applyCutoffs. It is recommended to estimate, and possibly adjust, population-specific separation cutoffs by running estCutoffs prior to this.
  3. plotYields, plotEvents and plotMahal aim to guide selection of devoncolution parameters and to give a sense of the resulting barcode assignment quality.
  4. lastly, population-wise FCS files are written from the dbFrame with outFCS.

3.1 Debarcoding work-flow

3.1.1 assignPrelim: Assignment of preliminary IDs

The debarcoding process commences by assigning each event a preliminary barcode ID. assignPrelim thereby takes either a binary barcoding scheme or a vector of numeric masses as input, and accordingly assigns each event the appropirate row name or mass as ID. FCS files are read into R with read.FCS of the flowCore package, and are represented as an object of class flowFrame:

data(sample_ff)
sample_ff

The debarcoding scheme should be a binary table with sample IDs as row and numeric barcode masses as column names:

data(sample_key)
sample_key
##    102 104 105 106 108 110
## A1   1   1   1   0   0   0
## A2   1   1   0   1   0   0
## A3   1   1   0   0   1   0
## A4   1   1   0   0   0   1
## A5   1   0   1   1   0   0
## B1   1   0   1   0   1   0
## B2   1   0   1   0   0   1
## B3   1   0   0   1   1   0
## B4   1   0   0   1   0   1
## B5   1   0   0   0   1   1
## C1   0   1   1   1   0   0
## C2   0   1   1   0   1   0
## C3   0   1   1   0   0   1
## C4   0   1   0   1   1   0
## C5   0   1   0   1   0   1
## D1   0   1   0   0   1   1
## D2   0   0   1   1   1   0
## D3   0   0   1   1   0   1
## D4   0   0   1   0   1   1
## D5   0   0   0   1   1   1

Provided with a flowFrame and a compatible barcoding scheme (barcode masses must occur in the parameters of the flowFrame), assignPrelim will return a dbFrame containing exprs from the input flowFrame, a numeric or character vector of event assignments in slot bc_ids, separations between barcode populations on the normalized scale in slot deltas, normalized barcode intensities in slot normed_bcs, and the counts and yields matrices. Measurement intensities are normalized by population such that each is scaled to the 95% quantile of asinh transformed measurement intensities of events assigned to the respective barcode population.

re <- assignPrelim(x=sample_ff, y=sample_key, verbose=FALSE)
re
## dbFrame objectect with
## 20000 events, 6 observables and 20 barcodes:
## 
## Current assignments:
##       0 event(s) unassigned                                                                           
## ID    A1   A2   A3   A4   A5   B1   B2   B3   B4   B5   C1   C2   C3   C4  
## Count 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
##                                    
## ID    C5   D1   D2   D3   D4   D5  
## Count 1000 1000 1000 1000 1000 1000

3.1.2 estCutoffs: Estimation of separation cutoffs

As opposed to a single global cutoff, estCutoffs will estimate a sample-specific cutoff to deal with barcode population cell yields that decline in an asynchronous fashion. Thus, the choice of thresholds for the distance between negative and positive barcode populations can be i) automated and ii) independent for each barcode. Nevertheless, reviewing the yield plots (see below), checking and possibly refining separation cutoffs is advisable.

For the estimation of cutoff parameters we consider yields upon debarcoding as a function of the applied cutoffs. Commonly, this function will be characterized by an initial weak decline, where doublets are excluded, and subsequent rapid decline in yields to zero. Inbetween, low numbers of counts with intermediate barcode separation give rise to a plateau. The separation cutoff value should be chosen such that it appropriately balances confidence in barcode assignment and cell yield. We thus fit the yields function, its first and second derivative, and compute the first turning point, marking the on-set of the plateu regime, as an adequte cutoff estimate.

re <- estCutoffs(x=re, verbose=FALSE)
re
## dbFrame objectect with
## 20000 events, 6 observables and 20 barcodes:
## 
## Current assignments:
##       0 event(s) unassigned                                                                           
## ID    A1   A2   A3   A4   A5   B1   B2   B3   B4   B5   C1   C2   C3   C4  
## Count 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
##                                    
## ID    C5   D1   D2   D3   D4   D5  
## Count 1000 1000 1000 1000 1000 1000
## 
## Separation cutoffs:                                                                            
## ID     A1   A2   A3   A4   A5   B1   B2   B3   B4   B5   C1   C2   C3   C4  
## Cutoff 0.26 0.33 0.30 0.16 0.34 0.23 0.30 0.29 0.37 0.31 0.38 0.27 0.27 0.17
##                                     
## ID     C5   D1   D2   D3   D4   D5  
## Cutoff 0.17 0.29 0.22 0.17 0.15 0.19
## 
## Yields upon debarcoding:
##       72.62% overall yield                                                                       
## ID    A1    A2    A3    A4    A5    B1    B2    B3    B4    B5    C1   
## Yield 61.6% 58.6% 65.3% 76.5% 66.1% 66.7% 74.9% 69.5% 70.9% 76.6% 59.6%
##                                                            
## ID    C2    C3    C4    C5    D1    D2    D3    D4    D5   
## Yield 70.5% 75.6% 77.3% 81.7% 76.5% 79.3% 80.1% 84.2% 80.8%

3.1.3 applyCutoffs: Applying deconvolution parameters

Once preliminary assignments have been made, applyCutoffs will apply the deconvolution parameters: Outliers are filtered by a Mahalanobis distance threshold, which takes into account each population’s covariance, and doublets are removed by excluding events from a population if the separation between their positive and negative signals fall below a separation cutoff. These thresholds are held in the sep_cutoffs and mhl_cutoff slots of the dbFrame. By default, applyCutoffs will try to access the sep_cutoffs in the provided dbFrame, requiring having run estCutoffs prior to this. Alternatively, a numeric vector of cutoff values or a single, global value may be specified. In either case, it is highly recommended to thoroughly review the yields plot (see above), as the choice of separation cutoffs will determine debarcoding quality and cell yield.

# use global separation cutoff
applyCutoffs(x=re, sep_cutoffs=0.35)

# use population-specific cutoffs
re <- applyCutoffs(x=re)

3.1.4 outFCS: Output population-wise FCS files

Once event assignments have been finalized, a separate FCS file can be written for each population by running outFCS. If option out_nms=NULL (the default), the respective population`s ID in the barcoding scheme will be used as file name. Alternatively, an ordered character vector or a 2 column CSV with sample IDs and the desired file names may be specified as a naming scheme.

outFCS(x=re)
## *** 21 FCS files created in

3.1.5 plotYields: Selecting barcode separation cutoffs

For each barcode, plotYields will show the distribution of barcode separations and yields upon debarcoding as a function of separation cutoffs. If available, the currently used separation cutoff as well as its resulting yield within the population is indicated in the plot’s main title.

plotYields(x=re, which="C1")

Option which=0 will render a summary plot of all barcodes. Here, the overall yield achieved by applying the current set of cutoff values will be shown. All yield functions should behave as described above: decline, stagnation, decline. Convergence to 0 yield at low cutoffs is a strong indicator that staining in this channel did not work, and excluding the channel entirely is sensible in this case. It is thus recommended to always view the all-barcodes yield plot to eliminate uninformative populations, since small populations may cause difficulties when computing spill estimates.

plotYields(x=re, which=0, legend=FALSE)

3.1.6 plotEvents: Normalized intensities

Normalized intensities for a barcode can be viewed with plotEvents. Here, each event corresponds to the intensities plotted on a vertical line at a given point along the x-axis. Option which=0 will display unassigned events, and the number of events shown for a given sample may be varied via n_events. If which="all", the function will render an event plot for all IDs (including 0) with events assigned.

# event plot for unassigned events
plotEvents(x=re, which=0, n_events=1000)

plotEvents(x=re, which="D1", n_events=500)

3.1.7 plotMahal: All barcode biaxial plot

Function plotMahal will plot all inter-barcode interactions for the population specified with argument which. Events are colored by their Mahalanobis distance. NOTE: For more than 7 barcodes (up to 128 samples) the function will render an error, as this visualization is infeasible and hardly informative. Using the default Mahalanobis cutoff value of 30 is recommended in such cases.

plotMahal(x=re, which="A5")

4 Compensation

CATALYST performs compensation via a two-step approach comprising:

  1. identification of single positive populations via single-cell debarcoding (SCD) of single-stained beads (or cells)
  2. estimation of a spillover matrix (SM) from the populations identified, followed by compensation via multiplication of measurement intensities by its inverse, the compensation matrix (CM).

As in conventional flow cytometry, we can model spillover linearly, with the channel stained for as predictor, and spill-effected channels as response. Thus, the intensity observed in a given channel \(j\) are a linear combination of its real signal and contributions of other channels that spill into it. Let \(s_{ij}\) denote the proportion of channel \(j\) signal that is due to channel \(i\), and \(w_j\) the set of channels that spill into channel \(j\). Then

\[I_{j, observed}\; = I_{j, real} + \sum_{i\in w_j}{s_{ij}}\]

In matrix notation, measurement intensities may be viewed as the convolution of real intensities and a spillover matrix with dimensions number of events times number of measurement parameters:

\[I_{observed}\; = I_{real} \cdot SM\]

Therefore, we can estimate the real signal, \(I_{real}\;\), as:

\[I_{real} = I_{observed}\; \cdot {SM}^{-1} = I_{observed}\; \cdot CM\] where \(\text{SM}^{-1}\) is termed compensation matrix (CM).

Because any signal not in a single stain experiment’s primary channel \(j\) results from channel crosstalk, each spill entry \(s_{ij}\) can be approximated by the slope of a linear regression with channel \(j\) signal as the response, and channel \(i\) signals as the predictors, where \(i\in w_j\). To facilitate robust estimates, we calculate this as the slope of a line through the medians (or trimmed means) of stained and unstained populations, \(m_j^+\) and \(m_i^+\), respectively. The medians (or trimmed means) computed from events that are i) negative in the respective channels; and, ii) not assigned to interacting channels; and, iii) not unassigned, \(m_j^-\) and \(m_i^-\), respectively, are subtracted as to account for background according to:

\[s_{ij} = \frac{m_j^+-m_j^-}{m_i^+-m_i^-}\]

On the basis of their additive nature, spill values are estimated independently for every pair of interacting channels. The current framework exclusively takes into consideration interactions that are sensible from a chemical and physical point of view:

Lastly, the SM’s diagonal entries \(s_{ii}\) are set to 1 so that spill is relative to the total signal measured in a given channel. The list of mass channels that may contain isotopic contaminatons are shown below.

List of isotopes available for each metal used in CyTOF
In addition to \(M\pm1\) and \(M+16\) channels, these mass channels are considered during estimation of spill to capture channel crosstalk that is due to isotopic contanimations (3).
Metal Isotope masses
La 138, 139
Pr 141
Nd 142, 143, 144, 145, 146, 148, 150
Sm 144, 147, 148, 149, 150, 152, 154
Eu 151, 153
Gd 152, 154, 155, 156, 157, 158, 160
Dy 156, 158, 160, 161, 162, 163, 164
Er 162, 164, 166, 167, 168, 170
Tb 159
Ho 165
Yb 168, 170, 171, 172, 173, 174, 176
Tm 169
Lu 175, 176

4.1 Compensation work-flow

4.1.1 computeSpillmat: Estimation of the spillover matrix

Given a flowFrame of single-stained beads (or cells) and a numeric vector specifying the masses stained for, computeSpillmat estimates the spillover matrix as described above. Spill values are affected my the method chosen for their estimation, that is "median" or "mean", and, in the latter case, the specified trim percentage. The process of adjusting these options and reviewing the compensated data may iterative until compensation is satisfactory

# get single-stained control samples
data(ss_exp)
# specify mass channels stained for
bc_ms <- c(139, 141:156, 158:176)
# debarcode
re <- assignPrelim(x=ss_exp, y=bc_ms, verbose=FALSE)
re <- estCutoffs(x=re, verbose=FALSE)
re <- applyCutoffs(x=re)
# compute spillover matrix
spillMat <- computeSpillmat(x=re)

4.1.2 estTrim: Estimation of an optimal trim value

To optimize results achieved upon compensation, estTrim will estimate the SM for a range of trim values, and evaluate, for each barcode population, the sum over squared medians of each negative channel upon compensation. Along with an optimal trim value, the function will return a figure of population- and channel-wise median counts for each trim value. The returned value is the one that minimizes this sum. Nevertheless, it may be worth chosing a trim value that gives rise to compensated data that is centered around 0 at the cost of a higher sum of squared medians. It is thus recommended to view the diagnostic plot to check the selected value, and potentially choose another. For example, in the figure below, the minimal sum of squares is achieved with a trim value of 0.4 while 0.2 appears to be a better choice as populations are kept from highly positive or negative medians.

# estimate trim value minimizing sum of squared 
# population- and channel-wise medians upon compensation
estTrim(x=re, min=0.05, max=0.11)
## Warning: We recommend that you use the dev version of ggplot2 with `ggplotly()`
## Install it with: `devtools::install_github('hadley/ggplot2')`

4.1.3 plotSpillmat: Spillover matrix heat map

plotSpillmat provides a visualization of estimated spill percentages as a heat map. Channels without a single-antibody stained control are annotated in grey, and colours are ramped to the highest spillover value present. Option annotate=TRUE (the default) will display spill values inside each bin, and the total amount of spill caused and received by each channel on the top and to the right, respectively.

spillMat <- computeSpillmat(x=re, trim=0.08)
plotSpillmat(bc_ms=bc_ms, SM=spillMat)

4.1.4 compCytof: Compensation of mass cytometry data

Assuming a linear spillover, compCytof compensates mass spectrometry based experiments using a provided spillover matrix. If the spillover matrix (SM) does not contain the same set of columns as the input experiment, it will be adapted according to the following rules:

  1. columns present in the SM but not in the input data will be removed from it
  2. non-metal columns present in the input but not in the SM will be added such that they do neither receive nor cause spill
  3. metal columns that have the same mass as a channel present in the SM will receive (but not emit) spillover according to that channel
  4. if an added channel could potentially receive spillover (as it has +/-1M or +16M of, or is of the same metal type as another channel measured), a warning will be issued as there could be spillover interactions that have been missed and may lead to faulty compensation

If out_path=NULL (the default), the function will return a flowFrame of the compensated data. Else, compensated data will be written to the specified location as FCS 3.0 standard files. Multiple data sets may be corrected based on the same spill estimates if the input x is a character string specifying the location of the FCS files to be compensated.

data(mp_cells)
comped_cells <- compCytof(x=mp_cells, y=spillMat)
## WARNING: Compensation is likely to be inaccurate.
##          Spill values for the following interactions
##          have not been estimated:
## Ba138Di -> La139Di, Sm154Di
## Ce140Di -> La139Di, Pr141Di, Gd156Di
## Gd157Di -> Gd156Di, Gd158Di, Sm152Di, Sm154Di, Gd155Di, Gd160Di, Yb173Di

5 Appendix

5.1 The dbFrame class

Data returned by and used throughout debarcoding are stored in a debarcoding frame. An object of class dbFrame includes the following elements:

  • Event information, stored in a matrix, is passed from the input flowFrame specified in assignPrelim to the exprs slot.
  • The bc_key slot is a binary matrix with numeric masses as column names and sample names as row names. If supplied with a numeric vector of masses, assignPrelim will internally generate a concurrent representation.
  • bc_ids is a numeric or character vector of the ID assignments that have been made. If a given event’s separation falls below its separation cutoff, or above the population’s Mahalanobis distance cutoff, it will be give ID 0 for “unassigned”. Assignments can be manipulated with bc_ids<-.
  • The deltas slot contains for each event the separations between positive and nergative populations, that is, between the lowest positive and highest negative intesity.
  • normed_bcs are the barcode intensities normalized by population. Here, each event is scaled to the 95% quantile of the population it’s been assigned to. sep_cutoffs are applied to these normalized intensities.
  • Slots sep_cutoffs and mhl_cutoff contain the devoncolution parameters. These can be specified by standard replacement via sep_cutoffs<- and mhl_cutoff<-.
  • counts and yields are matrices of dimension (# samples)x(101). Each row in the counts matrix contains the number of events within a sample for which positive and negative populations are separated by a distance between in [0,0.01), …, [0.99,1], respectively. The percentage of events within a sample that will be obtained after applying a separation cutoff of 0, 0.01, …, 1, respectively, is given in yields.

For a brief overview, show(dbFrame) will display

  • the dimensionality of the measurement data and number of barcodes
  • current assignments in order of decreasing population size
  • current separation cutoffs (if available)
  • the average and per-population yield achieved upon debarcoding
    (if sep_cutoffs are specified)

References

1. R. Finck et al., Normalization of mass cytometry data with bead standards. Cytometry Part A. 83A, 483–494 (2013).

2. E. R. Zunder et al., Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nat. Protocols. 10, 316–333 (2015).

3. J. S. Coursey, D. J. Schwab, J. J. Tsai, R. A. Dragoset, Atomic weights and isotopic compositions (2015), (available at http://physics.nist.gov/Comp).