Often, clustering single-cell data to identify communities of cells with shared characteristics is a major goal of high-dimensional cytometry data analysis.
To do this, {tidytof}
provides the
tof_cluster()
verb. Several clustering methods are
implemented in {tidytof}
, including the following:
Each of these methods are wrapped by tof_cluster()
.
tof_cluster()
To demonstrate, we can apply the PhenoGraph clustering algorithm to
{tidytof}
’s built-in phenograph_data
. Note
that phenograph_data
contains 3000 total cells (1000 each
from 3 clusters identified in the original PhenoGraph
publication). For demonstration purposes, we also metacluster our
PhenoGraph clusters using k-means clustering.
data(phenograph_data)
set.seed(203L)
phenograph_clusters <-
phenograph_data |>
tof_preprocess() |>
tof_cluster(
cluster_cols = starts_with("cd"),
num_neighbors = 50L,
distance_function = "cosine",
method = "phenograph"
) |>
tof_metacluster(
cluster_col = .phenograph_cluster,
metacluster_cols = starts_with("cd"),
num_metaclusters = 3L,
method = "kmeans"
)
phenograph_clusters |>
dplyr::select(sample_name, .phenograph_cluster, .kmeans_metacluster) |>
head()
#> # A tibble: 6 × 3
#> sample_name .phenograph_cluster .kmeans_metacluster
#> <chr> <chr> <chr>
#> 1 H1_PhenoGraph_cluster1 6 2
#> 2 H1_PhenoGraph_cluster1 1 2
#> 3 H1_PhenoGraph_cluster1 6 2
#> 4 H1_PhenoGraph_cluster1 6 2
#> 5 H1_PhenoGraph_cluster1 6 2
#> 6 H1_PhenoGraph_cluster1 6 2
The outputs of both tof_cluster()
and
tof_metacluster()
are a tof_tbl
identical to
the input tibble, but now with the addition of an additional column (in
this case, “.phenograph_cluster” and “.kmeans_metacluster”) that encodes
the cluster id for each cell in the input tof_tbl
. Note
that all output columns added to a tibble or tof_tbl
by
{tidytof}
begin with a full-stop (“.”) to reduce the
likelihood of collisions with existing column names.
Because the output of tof_cluster
is a
tof_tbl
, we can use dplyr
’s count
method to assess the accuracy of our clustering procedure compared to
the original clustering from the PhenoGraph paper.
phenograph_clusters |>
dplyr::count(phenograph_cluster, .kmeans_metacluster, sort = TRUE)
#> # A tibble: 4 × 3
#> phenograph_cluster .kmeans_metacluster n
#> <chr> <chr> <int>
#> 1 cluster2 3 1000
#> 2 cluster3 1 1000
#> 3 cluster1 2 995
#> 4 cluster1 1 5
Here, we can see that our clustering procedure groups most cells from the same PhenoGraph cluster with one another (with a small number of mistakes).
To change which clustering algorithm tof_cluster
uses,
alter the method
flag.
# use the kmeans algorithm
phenograph_data |>
tof_preprocess() |>
tof_cluster(
cluster_cols = contains("cd"),
method = "kmeans"
)
# use the flowsom algorithm
phenograph_data |>
tof_preprocess() |>
tof_cluster(
cluster_cols = contains("cd"),
method = "flowsom"
)
To change the columns used to compute the clusters, change the
cluster_cols
flag. And finally, if you want to return a
one-column tibble
that only includes the cluster labels (as
opposed to the cluster labels added as a new column to the input
tof_tbl
), set augment
to
FALSE
.
sessionInfo()
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