Fitting the models and additional control of fitGAM in tradeSeq
Koen Van den Berge and Hector Roux de Bézieux
25/02/2020
Introduction
tradeSeq is an R package that allows
analysis of gene expression along trajectories. While it has been
developed and applied to single-cell RNA-sequencing (scRNA-seq) data,
its applicability extends beyond that, and also allows the analysis of,
e.g., single-cell ATAC-seq data along trajectories or bulk RNA-seq time
series datasets. For every gene in the dataset, tradeSeq
fits a generalized additive model (GAM) by building on the
mgcv R package. It then allows statistical inference on the
GAM by assessing contrasts of the parameters of the fitted GAM model,
aiding in interpreting complex datasets. All details about the
tradeSeq model and statistical tests are described in our
preprint [@VandenBerge2019a].
In this vignette, we analyze a subset of the data from [@Paul2015]. A SingleCellExperiment
object of the data has been provided with the tradeSeq
package and can be retrieved as shown below. The data and UMAP reduced
dimensions were derived from following the Monocle
3 vignette.
Installation
To install the package, simply run
if(!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("tradeSeq")Alternatively, the development version can be installed from GitHub at https://github.com/statOmics/tradeSeq.
Load data
library(tradeSeq)
library(RColorBrewer)
library(SingleCellExperiment)
library(slingshot)
# For reproducibility
RNGversion("3.5.0")
palette(brewer.pal(8, "Dark2"))
data(countMatrix, package = "tradeSeq")
counts <- as.matrix(countMatrix)
rm(countMatrix)
data(crv, package = "tradeSeq")
data(celltype, package = "tradeSeq")We find two lineages for this dataset. The trajectory can be
visualized using the plotGeneCount function, using either
the cluster labels or cell type to color the cells.
plotGeneCount(curve = crv, clusters = celltype,
title = "Colored by cell type")
Choosing K: a deeper dive into the output from evaluateK
We use a negative binomial generalized additive model (NB-GAM)
framework in tradeSeq to smooth each gene’s expression in
each lineage. Smoothers can be decomposed into a set of basis functions,
which are joined together at knot points, often simply called knots.
Ideally, the number of knots should be selected to reach an optimal
bias-variance trade-off for the smoother, where one explains as much
variability in the expression data as possible with only a few
regression coefficients. In order to guide that choice, we developed
diagnostic plots using the Akaike Information Criterion (AIC). This is
implemented in the evaluateK function in
tradeSeq. The function takes as input the expression count
matrix, and the trajectory information, which can be either a
SlingshotDataSet, or a matrix of pseudotimes and cell-level
weights from any trajectory inference object. The range of knots to
evaluate is provided with the knots argument. The minimum
allowed number of knots is \(3\). While
there is no boundary on the maximum number of knots, typically the
interesting range is around \(3\) to
\(10\) knots. The
evaluateK function will fit NB-GAM models for some random
subset of genes, provided by the nGenes argument, over the
range of knots that are provided, and return the AIC for each gene
fitted with each number of knots. It is generally a good idea to
evaluate this multiple times using different seeds (using the
set.seed function), to check whether the results are
reproducible across different gene subsets.
By default, evaluateK outputs diagnostic plots that
should help in deciding on an appropriate number of knots. If you want
to use the different diagnostic plots to choose the number of knots when
fitting the smoothers, you can disable to plotting option and store the
AIC values in an object.
Below, we use the Slingshot object to run the function.
### Based on Slingshot object
set.seed(6)
icMat <- evaluateK(counts = counts, sds = crv, k = 3:7, nGenes = 100,
verbose = FALSE, plot = TRUE)
print(icMat[1:2, ])
### Downstream of any trajectory inference method using pseudotime and cell weights
set.seed(7)
pseudotime <- slingPseudotime(crv, na=FALSE)
cellWeights <- slingCurveWeights(crv)
icMat2 <- evaluateK(counts = counts, pseudotime = pseudotime, cellWeights = cellWeights,
k=3:7, nGenes = 100, verbose = FALSE, plot = TRUE)The output graphics are organized into four panels. The left panel
plots a boxplot for each number of knots we wanted to evaluate. The
plotted values are the deviation from a gene’s AIC at that specific knot
value from the average AIC of that gene across all the knots under
evaluation. Typically, AIC values are somewhat higher for low number of
knots, and we expect them to decrease as the number of knots gets
higher. The two middle panels plot the average drop in AIC across all
genes. The middle left panel simply plots the average AIC, while the
middle right panel plots the change in AIC relative to the average AIC
at the lowest knot number (here, this is 3 knots, as can also be seen
from the plot since the relative AIC equals \(1\)). Finally, the right panel only plots a
subset of genes where the AIC value changes significantly across the
evaluated number of knots. Here, a significant change is defined as a
change in absolute value of at least \(2\), but this can be tuned using the
aicDiff argument to evaluateK. For the subset
of genes, a barplot is displayed that shows the number of genes that
have their lowest AIC at a specific knot value.
The middle panels show that the drop in AIC levels off if the number
of knots is increased beyond \(6\), and
we will choose that number of knots to fit the tradeSeq
models.
Fit additive models
After deciding on an appropriate number of knots, we can fit the
NB-GAM for each gene. Internally, tradeSeq builds on the
mgcv package by fitting additive models using the
gam function. The core fitting function,
fitGAM, will use cubic splines as basis functions, and it
tries to ensure that every lineage will end at a knot point of a
smoother. By default, we allow for \(6\) knots for every lineage, but this can
be changed with the nknots argument. More knots will allow
more flexibility, but also increase the risk of overfitting.
By default, the GAM model estimates one smoother for every lineage
using the negative binomial distribution. If you want to allow for other
fixed effects (e.g., batch effects), then an additional model matrix,
typically created using the model.matrix function, can be
provided with the U argument. The precise model definition
of the statistical model is described in our preprint [@VandenBerge2019a]. We use the effective
library size, estimated with TMM [@Robinson2010], as offset in the model. We
allow for alternatives by allowing a user-defined offset with the
offset argument.
Similar to evaluateK, fitGAM can either take a
SlingshotDataSet object as input (sds
argument), or a matrix of pseudotimes and cell-level weights
(pseudotime and cellWeights argument). By
default, the returned object will be a SingleCellExperiment
object that contains all essential output from the model fitting. Note,
that also a more extensive output may be requested by setting
sce=FALSE, but this is much less memory efficient, see
below in Section ‘tradeSeq list output’.
Because cells are assigned to a lineage based on their weights, the
result of fitGAM is stochastic. While this should have
limited impact on the overall results in practice, users are therefore
encouraged to use the set.seed function before running
fitGAM to ensure reproducibility of their analyses.
Below, we show two ways in which you can provide the required input
to fitGAM: downstream of any trajectory inference method
and downstream of slingshot. To follow progress with a
progress bar, set verbose=TRUE.
### Based on Slingshot object
set.seed(6)
sce <- fitGAM(counts = counts, sds = crv, nknots = 6, verbose = FALSE)
### Downstream of any trajectory inference method using pseudotime and cell weights
set.seed(7)
pseudotime <- slingPseudotime(crv, na = FALSE)
cellWeights <- slingCurveWeights(crv)
sce <- fitGAM(counts = counts, pseudotime = pseudotime, cellWeights = cellWeights,
nknots = 6, verbose = FALSE)Adding covariates to the model
For some datasets it can be useful to add covariates to the model,
e.g. batch effects. This can be done by creating a design matrix using
the model.matrix function, and providing it as input to
fitGAM using the U argument. Below, we
incorporate artificial batch effects from the model, as if the data were
derived from two different batches.
batch <- factor(rep(c("A", "B"), each = ncol(counts)/2))
U <- model.matrix(~batch)
sceBatch <- fitGAM(counts = counts,
U = U,
sds = crv,
nknots = 6,
verbose = FALSE)Parallel computing
If large datasets are being analyzed, fitGAM may be
running for quite some time. We have implemented support for
parallelization using BiocParallel, which can be activated
by setting parallel=TRUE. Parallelization options can be
provided through the BPPARAM argument, as shown below.
BPPARAM <- BiocParallel::bpparam()
BPPARAM # lists current options## class: MulticoreParam
## bpisup: FALSE; bpnworkers: 4; bptasks: 0; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
## bpexportglobals: TRUE; bpexportvariables: FALSE; bpforceGC: FALSE
## bpfallback: TRUE
## bplogdir: NA
## bpresultdir: NA
## cluster type: FORKBPPARAM$workers <- 2 # use 2 cores
sce <- fitGAM(counts = counts, pseudotime = pseudotime, cellWeights = cellWeights,
nknots = 6, verbose = FALSE, parallel=TRUE, BPPARAM = BPPARAM)Fitting only a subset of genes
It may be of interest to only fit the NB-GAM for a subset of genes,
but use the information across all genes to perform the normalization.
This can be achieved using the genes argument in
fitGAM, which accepts a numeric vector specifying the rows
of the count matrix for which the models should be fitted.
sce25 <- fitGAM(counts = counts, pseudotime = pseudotime, cellWeights = cellWeights,
nknots = 6, verbose = FALSE, genes = 1:25)Zero inflation
This dataset consists of UMI counts, and we do not expect zero
inflation to be a big problem. However, we also allow to fit zero
inflated negative binomial (ZINB) GAMs by providing observation-level
weights to fitGAM using the weights argument.
The weights must correspond to the posterior probability
that a count belongs to the count component of the ZINB distribution
[@VandenBerge2018]. In principle, these
weights can be calculated using any method of choice. The ZINB-WavE
vignette shows how to calculate these using the
zinbwave package.
Convergence issues on small or zero-inflated datasets
If you’re working with a dataset that has a limited number of cells,
or if you are incorporating zero inflation weights, the NB-GAMs may be
harder to fit, as noted by the warnings when running
fitGAM. In that case, the situation might improve if you
allow for more iterations in the GAM fitting. This can be done with the
control argument of fitGAM.
library(mgcv)## Loading required package: nlme##
## Attaching package: 'nlme'## The following object is masked from 'package:IRanges':
##
## collapse## This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.control <- gam.control()
control$maxit <- 1000 #set maximum number of iterations to 1K
# pass to control argument of fitGAM as below:
#
# gamList <- fitGAM(counts = counts,
# pseudotime = slingPseudotime(crv, na = FALSE),
# cellWeights = slingCurveWeights(crv),
# control = control)tradeSeq list output
The output from fitGAM will be different if one sets
sce=FALSE, and less memory efficient. Instead of a
SingleCellExperiment object, it will return a list with all
fitted mgcv models. Most functions we have discussed above
work exactly the same with the list output. However, the list output
functionality is a little bit bigger, and here we discuss some
capabilities that are only available with the list output.
gamList <- fitGAM(counts,
pseudotime = slingPseudotime(crv, na = FALSE),
cellWeights = slingCurveWeights(crv),
nknots = 6, sce = FALSE)First, one may explore the results of a model by requesting its summary.
summary(gamList[["Irf8"]])##
## Family: Negative Binomial(2.221)
## Link function: log
##
## Formula:
## y ~ -1 + U + s(t1, by = l1, bs = "cr", id = 1, k = nknots) +
## s(t2, by = l2, bs = "cr", id = 1, k = nknots) + offset(offset)
##
## Parametric coefficients:
## Estimate Std. Error z value Pr(>|z|)
## U -10.0555 0.5408 -18.59 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df Chi.sq p-value
## s(t1):l1 5.698 5.956 589.260 <2e-16 ***
## s(t2):l2 3.387 3.819 9.329 0.0454 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 12/13
## R-sq.(adj) = 0.533 Deviance explained = 64%
## -REML = 2027.4 Scale est. = 1 n = 2660Related to the associationTest, one can extract the
p-values generated by the mgcv package using the
getSmootherPvalues function. These p-values are derived
from a test that assesses the null hypothesis that all smoother
coefficients are equal to zero. Note, however, that their interpretation
is thus more complex. A significant lineage for a particular gene might
thus be the result of (a) a different mean expression in that lineage as
compared to the overall expression of that gene, or (b) significantly
varying expression along that lineage, even if the means are equal, or
(c) a combination of both. This function extracts the p-values
calculated by mgcv from the GAM, and will return
NA for genes that we were unable to fit properly.
Similarly, the test statistics may be extracted with
getSmootherTestStats. Since this dataset was pre-filtered
to only contain relevant genes, all p-values (test statistics) will be
very low (high). Note, that these functions are only applicable with the
list output of tradeSeq, and not with the
SingleCellExperiment output. We will therefore not evaluate
these here.
pvalLineage <- getSmootherPvalues(gamList)
statLineage <- getSmootherTestStats(gamList)Also, the list output could be a good starting point for users that want to develop their own tests. A number of tests have been implemented in tradeSeq, but researchers may be interested in other hypotheses that current implementations may not be able to address. We therefore welcome contributions on GitHub on novel tests based on the tradeSeq model. Similar, you may also request novel tests to be implemented in tradeSeq by the developers, preferably by adding an issue on the GitHub repository. If we feel that the suggested test is widely applicable, we will implement it in tradeSeq.
Session
sessionInfo()## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## Random number generation:
## RNG: Mersenne-Twister
## Normal: Inversion
## Sample: Rounding
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## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] mgcv_1.9-1 nlme_3.1-166
## [3] slingshot_2.15.0 TrajectoryUtils_1.15.0
## [5] princurve_2.1.6 SingleCellExperiment_1.29.0
## [7] SummarizedExperiment_1.37.0 Biobase_2.67.0
## [9] GenomicRanges_1.59.0 GenomeInfoDb_1.43.0
## [11] IRanges_2.41.0 S4Vectors_0.45.0
## [13] BiocGenerics_0.53.0 MatrixGenerics_1.19.0
## [15] matrixStats_1.4.1 RColorBrewer_1.1-3
## [17] tradeSeq_1.21.0 knitr_1.48
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 xfun_0.48 bslib_0.8.0
## [4] ggplot2_3.5.1 lattice_0.22-6 vctrs_0.6.5
## [7] tools_4.5.0 generics_0.1.3 parallel_4.5.0
## [10] tibble_3.2.1 fansi_1.0.6 highr_0.11
## [13] pkgconfig_2.0.3 Matrix_1.7-1 lifecycle_1.0.4
## [16] GenomeInfoDbData_1.2.13 farver_2.1.2 compiler_4.5.0
## [19] statmod_1.5.0 munsell_0.5.1 codetools_0.2-20
## [22] htmltools_0.5.8.1 sass_0.4.9 yaml_2.3.10
## [25] pillar_1.9.0 crayon_1.5.3 jquerylib_0.1.4
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## [34] locfit_1.5-9.10 tidyselect_1.2.1 digest_0.6.37
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## [40] fastmap_1.2.0 grid_4.5.0 colorspace_2.1-1
## [43] cli_3.6.3 SparseArray_1.7.0 magrittr_2.0.3
## [46] S4Arrays_1.7.0 utf8_1.2.4 withr_3.0.2
## [49] edgeR_4.5.0 scales_1.3.0 UCSC.utils_1.3.0
## [52] rmarkdown_2.28 XVector_0.47.0 httr_1.4.7
## [55] igraph_2.1.1 gridExtra_2.3 pbapply_1.7-2
## [58] evaluate_1.0.1 viridisLite_0.4.2 rlang_1.1.4
## [61] Rcpp_1.0.13 glue_1.8.0 jsonlite_1.8.9
## [64] R6_2.5.1 zlibbioc_1.53.0