README.md
In stemangiola/tidySCE: Brings SingleCellExperiment to the Tidyverse
tidySingleCellExperiment - part of tidytranscriptomics
Brings SingleCellExperiment to the tidyverse!
Website:
tidySingleCellExperiment
Please also have a look at
- tidySummarizedExperiment
for tidy manipulation of SummarizedExperiment objects)
- tidyseurat for tidy
manipulation of Seurat objects
- tidybulk for tidy bulk
RNA-seq data analysis
- tidygate for adding custom
gate information to your tibble
- tidyHeatmap for heatmaps
produced with tidy principles
Introduction
tidySingleCellExperiment provides a bridge between Bioconductor
single-cell packages [@amezquita2019orchestrating] and the tidyverse
[@wickham2019welcome]. It enables viewing the Bioconductor
SingleCellExperiment object as a tidyverse tibble, and provides
SingleCellExperiment-compatible dplyr, tidyr, ggplot and plotly
functions. This allows users to get the best of both Bioconductor and
tidyverse worlds.
Functions/utilities available
| SingleCellExperiment-compatible Functions | Description |
|-------------------------------------------|------------------------------------------------------------------------------------|
| all | After all tidySingleCellExperiment is a SingleCellExperiment object, just better |
| tidyverse Packages | Description |
|--------------------|----------------------------------------------------|
| dplyr | All dplyr tibble functions (e.g. select) |
| tidyr | All tidyr tibble functions (e.g. pivot_longer) |
| ggplot2 | ggplot (ggplot) |
| plotly | plot_ly (plot_ly) |
| Utilities | Description |
|-------------------|------------------------------------------------------------------|
| as_tibble | Convert cell-wise information to a tbl_df |
| join_features | Add feature-wise information, returns a tbl_df |
| aggregate_cells | Aggregate cell gene-transcription abundance as pseudobulk tissue |
Installation
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("tidySingleCellExperiment")
Load libraries used in this vignette.
# Bioconductor single-cell packages
library(scater)
library(scran)
library(SingleR)
library(SingleCellSignalR)
# Tidyverse-compatible packages
library(purrr)
library(magrittr)
library(tidyHeatmap)
# Both
library(tidySingleCellExperiment)
Data representation of tidySingleCellExperiment
This is a SingleCellExperiment object but it is evaluated as a tibble.
So it is compatible both with SingleCellExperiment and tidyverse.
data(pbmc_small, package="tidySingleCellExperiment")
It looks like a tibble
pbmc_small
## # A SingleCellExperiment-tibble abstraction: 80 × 17
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
## <chr> <fct> <dbl> <int> <fct> <fct> <chr>
## 1 ATGC… SeuratPro… 70 47 0 A g2
## 2 CATG… SeuratPro… 85 52 0 A g1
## 3 GAAC… SeuratPro… 87 50 1 B g2
## 4 TGAC… SeuratPro… 127 56 0 A g2
## 5 AGTC… SeuratPro… 173 53 0 A g2
## 6 TCTG… SeuratPro… 70 48 0 A g1
## 7 TGGT… SeuratPro… 64 36 0 A g1
## 8 GCAG… SeuratPro… 72 45 0 A g1
## 9 GATA… SeuratPro… 52 36 0 A g1
## 10 AATG… SeuratPro… 100 41 0 A g1
## # ℹ 70 more rows
## # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
## # PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
## # tSNE_2 <dbl>
But it is a SingleCellExperiment object after all
assay(pbmc_small, "counts")[1:5, 1:5]
## 5 x 5 sparse Matrix of class "dgCMatrix"
## ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA
## MS4A1 . . . .
## CD79B 1 . . .
## CD79A . . . .
## HLA-DRA . 1 . .
## TCL1A . . . .
## AGTCAGACTGCACA
## MS4A1 .
## CD79B .
## CD79A .
## HLA-DRA 1
## TCL1A .
The SingleCellExperiment object’s tibble visualisation can be turned
off, or back on at any time.
# Turn off the tibble visualisation
options("restore_SingleCellExperiment_show" = TRUE)
pbmc_small
## class: SingleCellExperiment
## dim: 230 80
## metadata(0):
## assays(2): counts logcounts
## rownames(230): MS4A1 CD79B ... SPON2 S100B
## rowData names(5): vst.mean vst.variance vst.variance.expected
## vst.variance.standardized vst.variable
## colnames(80): ATGCCAGAACGACT CATGGCCTGTGCAT ... GGAACACTTCAGAC
## CTTGATTGATCTTC
## colData names(9): orig.ident nCount_RNA ... file ident
# Turn on the tibble visualisation
options("restore_SingleCellExperiment_show" = FALSE)
Annotation polishing
We may have a column that contains the directory each run was taken
from, such as the “file” column in pbmc_small.
pbmc_small$file[1:5]
## [1] "../data/sample2/outs/filtered_feature_bc_matrix/"
## [2] "../data/sample1/outs/filtered_feature_bc_matrix/"
## [3] "../data/sample2/outs/filtered_feature_bc_matrix/"
## [4] "../data/sample2/outs/filtered_feature_bc_matrix/"
## [5] "../data/sample2/outs/filtered_feature_bc_matrix/"
We may want to extract the run/sample name out of it into a separate
column. Tidyverse extract can be used to convert a character column
into multiple columns using regular expression groups.
# Create sample column
pbmc_small_polished <-
pbmc_small |>
extract(file, "sample", "../data/([a-z0-9]+)/outs.+", remove=FALSE)
# Reorder to have sample column up front
pbmc_small_polished |>
select(sample, everything())
## # A SingleCellExperiment-tibble abstraction: 80 × 18
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell sample orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
## <chr> <chr> <fct> <dbl> <int> <fct> <fct>
## 1 ATGC… sampl… SeuratPro… 70 47 0 A
## 2 CATG… sampl… SeuratPro… 85 52 0 A
## 3 GAAC… sampl… SeuratPro… 87 50 1 B
## 4 TGAC… sampl… SeuratPro… 127 56 0 A
## 5 AGTC… sampl… SeuratPro… 173 53 0 A
## 6 TCTG… sampl… SeuratPro… 70 48 0 A
## 7 TGGT… sampl… SeuratPro… 64 36 0 A
## 8 GCAG… sampl… SeuratPro… 72 45 0 A
## 9 GATA… sampl… SeuratPro… 52 36 0 A
## 10 AATG… sampl… SeuratPro… 100 41 0 A
## # ℹ 70 more rows
## # ℹ 11 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
## # ident <fct>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>,
## # tSNE_1 <dbl>, tSNE_2 <dbl>
Preliminary plots
Set colours and theme for plots.
# Use colourblind-friendly colours
friendly_cols <- dittoSeq::dittoColors()
# Set theme
custom_theme <-
list(
scale_fill_manual(values=friendly_cols),
scale_color_manual(values=friendly_cols),
theme_bw() +
theme(
panel.border=element_blank(),
axis.line=element_line(),
panel.grid.major=element_line(size=0.2),
panel.grid.minor=element_line(size=0.1),
text=element_text(size=12),
legend.position="bottom",
aspect.ratio=1,
strip.background=element_blank(),
axis.title.x=element_text(margin=margin(t=10, r=10, b=10, l=10)),
axis.title.y=element_text(margin=margin(t=10, r=10, b=10, l=10))
)
)
## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
We can treat pbmc_small_polished as a tibble for plotting.
Here we plot number of features per cell.
pbmc_small_polished |>
ggplot(aes(nFeature_RNA, fill=groups)) +
geom_histogram() +
custom_theme
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Here we plot total features per cell.
pbmc_small_polished |>
ggplot(aes(groups, nCount_RNA, fill=groups)) +
geom_boxplot(outlier.shape=NA) +
geom_jitter(width=0.1) +
custom_theme
Here we plot abundance of two features for each group.
pbmc_small_polished |>
join_features(features=c("HLA-DRA", "LYZ")) |>
ggplot(aes(groups, .abundance_counts + 1, fill=groups)) +
geom_boxplot(outlier.shape=NA) +
geom_jitter(aes(size=nCount_RNA), alpha=0.5, width=0.2) +
scale_y_log10() +
custom_theme
## tidySingleCellExperiment says: join_features produces duplicate cell names to accomadate the long data format. For this reason, a data frame is returned for independent data analysis. Assay feature abundance is appended as .abundance_counts and .abundance_logcounts.
Preprocess the dataset
We can also treat pbmc_small_polished as a SingleCellExperiment
object and proceed with data processing with Bioconductor packages, such
as scran [@lun2016pooling] and scater [@mccarthy2017scater].
# Identify variable genes with scran
variable_genes <-
pbmc_small_polished |>
modelGeneVar() |>
getTopHVGs(prop=0.1)
# Perform PCA with scater
pbmc_small_pca <-
pbmc_small_polished |>
runPCA(subset_row=variable_genes)
## Warning in check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - : more
## singular values/vectors requested than available
## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
## TRUE, : You're computing too large a percentage of total singular values, use a
## standard svd instead.
## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
## TRUE, : did not converge--results might be invalid!; try increasing work or
## maxit
pbmc_small_pca
## # A SingleCellExperiment-tibble abstraction: 80 × 18
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
## <chr> <fct> <dbl> <int> <fct> <fct> <chr>
## 1 ATGC… SeuratPro… 70 47 0 A g2
## 2 CATG… SeuratPro… 85 52 0 A g1
## 3 GAAC… SeuratPro… 87 50 1 B g2
## 4 TGAC… SeuratPro… 127 56 0 A g2
## 5 AGTC… SeuratPro… 173 53 0 A g2
## 6 TCTG… SeuratPro… 70 48 0 A g1
## 7 TGGT… SeuratPro… 64 36 0 A g1
## 8 GCAG… SeuratPro… 72 45 0 A g1
## 9 GATA… SeuratPro… 52 36 0 A g1
## 10 AATG… SeuratPro… 100 41 0 A g1
## # ℹ 70 more rows
## # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, sample <chr>,
## # ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>, PC5 <dbl>,
## # tSNE_1 <dbl>, tSNE_2 <dbl>
If a tidyverse-compatible package is not included in the
tidySingleCellExperiment collection, we can use as_tibble to
permanently convert tidySingleCellExperiment into a tibble.
# Create pairs plot with GGally
pbmc_small_pca |>
as_tibble() |>
select(contains("PC"), everything()) |>
GGally::ggpairs(columns=1:5, ggplot2::aes(colour=groups)) +
custom_theme
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
Identify clusters
We can proceed with cluster identification with scran.
pbmc_small_cluster <- pbmc_small_pca
# Assign clusters to the 'colLabels' of the SingleCellExperiment object
colLabels(pbmc_small_cluster) <-
pbmc_small_pca |>
buildSNNGraph(use.dimred="PCA") |>
igraph::cluster_walktrap() %$%
membership |>
as.factor()
## Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
## detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# Reorder columns
pbmc_small_cluster |> select(label, everything())
## # A SingleCellExperiment-tibble abstraction: 80 × 19
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell label orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
## <chr> <fct> <fct> <dbl> <int> <fct> <fct>
## 1 ATGCC… 2 SeuratPro… 70 47 0 A
## 2 CATGG… 2 SeuratPro… 85 52 0 A
## 3 GAACC… 2 SeuratPro… 87 50 1 B
## 4 TGACT… 1 SeuratPro… 127 56 0 A
## 5 AGTCA… 2 SeuratPro… 173 53 0 A
## 6 TCTGA… 2 SeuratPro… 70 48 0 A
## 7 TGGTA… 1 SeuratPro… 64 36 0 A
## 8 GCAGC… 2 SeuratPro… 72 45 0 A
## 9 GATAT… 2 SeuratPro… 52 36 0 A
## 10 AATGT… 2 SeuratPro… 100 41 0 A
## # ℹ 70 more rows
## # ℹ 12 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
## # sample <chr>, ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>,
## # PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>
And interrogate the output as if it was a regular tibble.
# Count number of cells for each cluster per group
pbmc_small_cluster |>
count(groups, label)
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
## # A tibble: 8 × 3
## groups label n
## <chr> <fct> <int>
## 1 g1 1 12
## 2 g1 2 14
## 3 g1 3 14
## 4 g1 4 4
## 5 g2 1 10
## 6 g2 2 11
## 7 g2 3 10
## 8 g2 4 5
We can identify and visualise cluster markers combining
SingleCellExperiment, tidyverse functions and tidyHeatmap
[@mangiola2020tidyheatmap]
# Identify top 10 markers per cluster
marker_genes <-
pbmc_small_cluster |>
findMarkers(groups=pbmc_small_cluster$label) |>
as.list() |>
map(~ .x |>
head(10) |>
rownames()) |>
unlist()
# Plot heatmap
pbmc_small_cluster |>
join_features(features=marker_genes) |>
group_by(label) |>
heatmap(.feature, .cell, .abundance_counts, .scale="column")
## tidySingleCellExperiment says: join_features produces duplicate cell names to accomadate the long data format. For this reason, a data frame is returned for independent data analysis. Assay feature abundance is appended as .abundance_counts and .abundance_logcounts.
## tidyHeatmap says: (once per session) from release 1.7.0 the scaling is set to "none" by default. Please use scale = "row", "column" or "both" to apply scaling
## Warning: The `.scale` argument of `heatmap()` is deprecated as of tidyHeatmap 1.7.0.
## ℹ Please use scale (without dot prefix) instead: heatmap(scale = ...)
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
Reduce dimensions
We can calculate the first 3 UMAP dimensions using the
SingleCellExperiment framework and scater.
pbmc_small_UMAP <-
pbmc_small_cluster |>
runUMAP(ncomponents=3)
And we can plot the result in 3D using plotly.
pbmc_small_UMAP |>
plot_ly(
x=~`UMAP1`,
y=~`UMAP2`,
z=~`UMAP3`,
color=~label,
colors=friendly_cols[1:4]
)
plotly screenshot
Cell type prediction
We can infer cell type identities using SingleR [@aran2019reference]
and manipulate the output using tidyverse.
# Get cell type reference data
blueprint <- celldex::BlueprintEncodeData()
# Infer cell identities
cell_type_df <-
assays(pbmc_small_UMAP)$logcounts |>
Matrix::Matrix(sparse = TRUE) |>
SingleR::SingleR(
ref = blueprint,
labels = blueprint$label.main,
method = "single"
) |>
as.data.frame() |>
as_tibble(rownames="cell") |>
select(cell, first.labels)
# Join UMAP and cell type info
data(cell_type_df)
pbmc_small_cell_type <-
pbmc_small_UMAP |>
left_join(cell_type_df, by="cell")
## Warning in is_sample_feature_deprecated_used(x, .cols):
## tidySingleCellExperiment says: from version 1.3.1, the special columns
## including cell id (colnames(se)) has changed to ".cell". This dataset is
## returned with the old-style vocabulary (cell), however, we suggest to update
## your workflow to reflect the new vocabulary (.cell).
# Reorder columns
pbmc_small_cell_type |>
select(cell, first.labels, everything())
## Warning in is_sample_feature_deprecated_used(.data, .cols):
## tidySingleCellExperiment says: from version 1.3.1, the special columns
## including cell id (colnames(se)) has changed to ".cell". This dataset is
## returned with the old-style vocabulary (cell), however, we suggest to update
## your workflow to reflect the new vocabulary (.cell).
## # A SingleCellExperiment-tibble abstraction: 80 × 23
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## cell first.labels orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8
## <chr> <chr> <fct> <dbl> <int> <fct>
## 1 ATGCCAGAACGA… CD4+ T-cells SeuratPro… 70 47 0
## 2 CATGGCCTGTGC… CD8+ T-cells SeuratPro… 85 52 0
## 3 GAACCTGATGAA… CD8+ T-cells SeuratPro… 87 50 1
## 4 TGACTGGATTCT… CD4+ T-cells SeuratPro… 127 56 0
## 5 AGTCAGACTGCA… CD4+ T-cells SeuratPro… 173 53 0
## 6 TCTGATACACGT… CD4+ T-cells SeuratPro… 70 48 0
## 7 TGGTATCTAAAC… CD4+ T-cells SeuratPro… 64 36 0
## 8 GCAGCTCTGTTT… CD4+ T-cells SeuratPro… 72 45 0
## 9 GATATAACACGC… CD4+ T-cells SeuratPro… 52 36 0
## 10 AATGTTGACAGT… CD4+ T-cells SeuratPro… 100 41 0
## # ℹ 70 more rows
## # ℹ 17 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>,
## # file <chr>, sample <chr>, ident <fct>, label <fct>, PC1 <dbl>, PC2 <dbl>,
## # PC3 <dbl>, PC4 <dbl>, PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>, UMAP1 <dbl>,
## # UMAP2 <dbl>, UMAP3 <dbl>
We can easily summarise the results. For example, we can see how cell
type classification overlaps with cluster classification.
# Count number of cells for each cell type per cluster
pbmc_small_cell_type |>
count(label, first.labels)
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
## # A tibble: 11 × 3
## label first.labels n
## <fct> <chr> <int>
## 1 1 CD4+ T-cells 2
## 2 1 CD8+ T-cells 8
## 3 1 NK cells 12
## 4 2 B-cells 10
## 5 2 CD4+ T-cells 6
## 6 2 CD8+ T-cells 2
## 7 2 Macrophages 1
## 8 2 Monocytes 6
## 9 3 Macrophages 1
## 10 3 Monocytes 23
## 11 4 Erythrocytes 9
We can easily reshape the data for building information-rich faceted
plots.
pbmc_small_cell_type |>
# Reshape and add classifier column
pivot_longer(
cols=c(label, first.labels),
names_to="classifier", values_to="label"
) |>
# UMAP plots for cell type and cluster
ggplot(aes(UMAP1, UMAP2, color=label)) +
geom_point() +
facet_wrap(~classifier) +
custom_theme
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
We can easily plot gene correlation per cell category, adding
multi-layer annotations.
pbmc_small_cell_type |>
# Add some mitochondrial abundance values
mutate(mitochondrial=rnorm(dplyr::n())) |>
# Plot correlation
join_features(features=c("CST3", "LYZ"), shape="wide") |>
ggplot(aes(CST3 + 1, LYZ + 1, color=groups, size=mitochondrial)) +
geom_point() +
facet_wrap(~first.labels, scales="free") +
scale_x_log10() +
scale_y_log10() +
custom_theme
## Warning in is_sample_feature_deprecated_used(x, .cols):
## tidySingleCellExperiment says: from version 1.3.1, the special columns
## including cell id (colnames(se)) has changed to ".cell". This dataset is
## returned with the old-style vocabulary (cell), however, we suggest to update
## your workflow to reflect the new vocabulary (.cell).
Nested analyses
A powerful tool we can use with tidySingleCellExperiment is tidyverse
nest. We can easily perform independent analyses on subsets of the
dataset. First we classify cell types into lymphoid and myeloid, and
then nest based on the new classification.
pbmc_small_nested <-
pbmc_small_cell_type |>
filter(first.labels != "Erythrocytes") |>
mutate(cell_class=dplyr::if_else(`first.labels` %in% c("Macrophages", "Monocytes"), "myeloid", "lymphoid")) |>
nest(data=-cell_class)
## Warning: There were 2 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `data = map(...)`.
## Caused by warning in `is_sample_feature_deprecated_used()`:
## ! tidySingleCellExperiment says: from version 1.3.1, the special columns including cell id (colnames(se)) has changed to ".cell". This dataset is returned with the old-style vocabulary (cell), however, we suggest to update your workflow to reflect the new vocabulary (.cell).
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.
pbmc_small_nested
## # A tibble: 2 × 2
## cell_class data
## <chr> <list>
## 1 lymphoid <SnglCllE[,40]>
## 2 myeloid <SnglCllE[,31]>
Now we can independently for the lymphoid and myeloid subsets (i) find
variable features, (ii) reduce dimensions, and (iii) cluster using both
tidyverse and SingleCellExperiment seamlessly.
pbmc_small_nested_reanalysed <-
pbmc_small_nested |>
mutate(data=map(
data, ~ {
.x <- runPCA(.x, subset_row=variable_genes)
variable_genes <-
.x |>
modelGeneVar() |>
getTopHVGs(prop=0.3)
colLabels(.x) <-
.x |>
buildSNNGraph(use.dimred="PCA") |>
igraph::cluster_walktrap() %$%
membership |>
as.factor()
.x |> runUMAP(ncomponents=3)
}
))
pbmc_small_nested_reanalysed
## # A tibble: 2 × 2
## cell_class data
## <chr> <list>
## 1 lymphoid <SnglCllE[,40]>
## 2 myeloid <SnglCllE[,31]>
We can then unnest and plot the new classification.
pbmc_small_nested_reanalysed |>
# Convert to tibble otherwise SingleCellExperiment drops reduced dimensions when unifying data sets.
mutate(data=map(data, ~ .x |> as_tibble())) |>
unnest(data) |>
# Define unique clusters
unite("cluster", c(cell_class, label), remove=FALSE) |>
# Plotting
ggplot(aes(UMAP1, UMAP2, color=cluster)) +
geom_point() +
facet_wrap(~cell_class) +
custom_theme
We can perform a large number of functional analyses on data subsets.
For example, we can identify intra-sample cell-cell interactions using
SingleCellSignalR [@cabello2020singlecellsignalr], and then compare
whether interactions are stronger or weaker across conditions. The code
below demonstrates how this analysis could be performed. It won’t work
with this small example dataset as we have just two samples (one for
each condition). But some example output is shown below and you can
imagine how you can use tidyverse on the output to perform t-tests and
visualisation.
pbmc_small_nested_interactions <-
pbmc_small_nested_reanalysed |>
# Unnest based on cell category
unnest(data) |>
# Create unambiguous clusters
mutate(integrated_clusters=first.labels |> as.factor() |> as.integer()) |>
# Nest based on sample
nest(data=-sample) |>
mutate(interactions=map(data, ~ {
# Produce variables. Yuck!
cluster <- colData(.x)$integrated_clusters
data <- data.frame(assays(.x) |> as.list() |> extract2(1) |> as.matrix())
# Ligand/Receptor analysis using SingleCellSignalR
data |>
cell_signaling(genes=rownames(data), cluster=cluster) |>
inter_network(data=data, signal=_, genes=rownames(data), cluster=cluster) %$%
`individual-networks` |>
map_dfr(~ bind_rows(as_tibble(.x)))
}))
pbmc_small_nested_interactions |>
select(-data) |>
unnest(interactions)
If the dataset was not so small, and interactions could be identified,
you would see something like below.
data(pbmc_small_nested_interactions)
pbmc_small_nested_interactions
## # A tibble: 100 × 9
## sample ligand receptor ligand.name receptor.name origin destination
## <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 sample1 cluster 1.PTMA cluster… PTMA VIPR1 clust… cluster 2
## 2 sample1 cluster 1.B2M cluster… B2M KLRD1 clust… cluster 2
## 3 sample1 cluster 1.IL16 cluster… IL16 CD4 clust… cluster 2
## 4 sample1 cluster 1.HLA-B cluster… HLA-B KLRD1 clust… cluster 2
## 5 sample1 cluster 1.CALM1 cluster… CALM1 VIPR1 clust… cluster 2
## 6 sample1 cluster 1.HLA-E cluster… HLA-E KLRD1 clust… cluster 2
## 7 sample1 cluster 1.GNAS cluster… GNAS VIPR1 clust… cluster 2
## 8 sample1 cluster 1.B2M cluster… B2M HFE clust… cluster 2
## 9 sample1 cluster 1.PTMA cluster… PTMA VIPR1 clust… cluster 3
## 10 sample1 cluster 1.CALM1 cluster… CALM1 VIPR1 clust… cluster 3
## # ℹ 90 more rows
## # ℹ 2 more variables: interaction.type <chr>, LRscore <dbl>
Aggregating cells
Sometimes, it is necessary to aggregate the gene-transcript abundance
from a group of cells into a single value. For example, when comparing
groups of cells across different samples with fixed-effect models.
In tidySingleCellExperiment, cell aggregation can be achieved using the
aggregate_cells function.
pbmc_small |>
aggregate_cells(groups, assays = "counts")
## class: SummarizedExperiment
## dim: 230 2
## metadata(0):
## assays(1): counts
## rownames(230): ACAP1 ACRBP ... ZNF330 ZNF76
## rowData names(0):
## colnames(2): g1 g2
## colData names(4): .aggregated_cells groups orig.ident file
stemangiola/tidySCE documentation built on Sept. 22, 2024, 10:05 p.m.
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tidySingleCellExperiment - part of tidytranscriptomics
Brings SingleCellExperiment to the tidyverse!
Website: tidySingleCellExperiment
Please also have a look at
- tidySummarizedExperiment for tidy manipulation of SummarizedExperiment objects)
- tidyseurat for tidy manipulation of Seurat objects
- tidybulk for tidy bulk RNA-seq data analysis
- tidygate for adding custom gate information to your tibble
- tidyHeatmap for heatmaps produced with tidy principles
Introduction
tidySingleCellExperiment provides a bridge between Bioconductor single-cell packages [@amezquita2019orchestrating] and the tidyverse [@wickham2019welcome]. It enables viewing the Bioconductor SingleCellExperiment object as a tidyverse tibble, and provides SingleCellExperiment-compatible dplyr, tidyr, ggplot and plotly functions. This allows users to get the best of both Bioconductor and tidyverse worlds.
Functions/utilities available
| SingleCellExperiment-compatible Functions | Description |
|-------------------------------------------|------------------------------------------------------------------------------------|
| all | After all tidySingleCellExperiment is a SingleCellExperiment object, just better |
| tidyverse Packages | Description |
|--------------------|----------------------------------------------------|
| dplyr | All dplyr tibble functions (e.g. select) |
| tidyr | All tidyr tibble functions (e.g. pivot_longer) |
| ggplot2 | ggplot (ggplot) |
| plotly | plot_ly (plot_ly) |
| Utilities | Description |
|-------------------|------------------------------------------------------------------|
| as_tibble | Convert cell-wise information to a tbl_df |
| join_features | Add feature-wise information, returns a tbl_df |
| aggregate_cells | Aggregate cell gene-transcription abundance as pseudobulk tissue |
Installation
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("tidySingleCellExperiment")
Load libraries used in this vignette.
# Bioconductor single-cell packages
library(scater)
library(scran)
library(SingleR)
library(SingleCellSignalR)
# Tidyverse-compatible packages
library(purrr)
library(magrittr)
library(tidyHeatmap)
# Both
library(tidySingleCellExperiment)
Data representation of tidySingleCellExperiment
This is a SingleCellExperiment object but it is evaluated as a tibble. So it is compatible both with SingleCellExperiment and tidyverse.
data(pbmc_small, package="tidySingleCellExperiment")
It looks like a tibble
pbmc_small
## # A SingleCellExperiment-tibble abstraction: 80 × 17
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
## <chr> <fct> <dbl> <int> <fct> <fct> <chr>
## 1 ATGC… SeuratPro… 70 47 0 A g2
## 2 CATG… SeuratPro… 85 52 0 A g1
## 3 GAAC… SeuratPro… 87 50 1 B g2
## 4 TGAC… SeuratPro… 127 56 0 A g2
## 5 AGTC… SeuratPro… 173 53 0 A g2
## 6 TCTG… SeuratPro… 70 48 0 A g1
## 7 TGGT… SeuratPro… 64 36 0 A g1
## 8 GCAG… SeuratPro… 72 45 0 A g1
## 9 GATA… SeuratPro… 52 36 0 A g1
## 10 AATG… SeuratPro… 100 41 0 A g1
## # ℹ 70 more rows
## # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
## # PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
## # tSNE_2 <dbl>
But it is a SingleCellExperiment object after all
assay(pbmc_small, "counts")[1:5, 1:5]
## 5 x 5 sparse Matrix of class "dgCMatrix"
## ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA
## MS4A1 . . . .
## CD79B 1 . . .
## CD79A . . . .
## HLA-DRA . 1 . .
## TCL1A . . . .
## AGTCAGACTGCACA
## MS4A1 .
## CD79B .
## CD79A .
## HLA-DRA 1
## TCL1A .
The SingleCellExperiment object’s tibble visualisation can be turned
off, or back on at any time.
# Turn off the tibble visualisation
options("restore_SingleCellExperiment_show" = TRUE)
pbmc_small
## class: SingleCellExperiment
## dim: 230 80
## metadata(0):
## assays(2): counts logcounts
## rownames(230): MS4A1 CD79B ... SPON2 S100B
## rowData names(5): vst.mean vst.variance vst.variance.expected
## vst.variance.standardized vst.variable
## colnames(80): ATGCCAGAACGACT CATGGCCTGTGCAT ... GGAACACTTCAGAC
## CTTGATTGATCTTC
## colData names(9): orig.ident nCount_RNA ... file ident
# Turn on the tibble visualisation
options("restore_SingleCellExperiment_show" = FALSE)
Annotation polishing
We may have a column that contains the directory each run was taken
from, such as the “file” column in pbmc_small.
pbmc_small$file[1:5]
## [1] "../data/sample2/outs/filtered_feature_bc_matrix/"
## [2] "../data/sample1/outs/filtered_feature_bc_matrix/"
## [3] "../data/sample2/outs/filtered_feature_bc_matrix/"
## [4] "../data/sample2/outs/filtered_feature_bc_matrix/"
## [5] "../data/sample2/outs/filtered_feature_bc_matrix/"
We may want to extract the run/sample name out of it into a separate
column. Tidyverse extract can be used to convert a character column
into multiple columns using regular expression groups.
# Create sample column
pbmc_small_polished <-
pbmc_small |>
extract(file, "sample", "../data/([a-z0-9]+)/outs.+", remove=FALSE)
# Reorder to have sample column up front
pbmc_small_polished |>
select(sample, everything())
## # A SingleCellExperiment-tibble abstraction: 80 × 18
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell sample orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
## <chr> <chr> <fct> <dbl> <int> <fct> <fct>
## 1 ATGC… sampl… SeuratPro… 70 47 0 A
## 2 CATG… sampl… SeuratPro… 85 52 0 A
## 3 GAAC… sampl… SeuratPro… 87 50 1 B
## 4 TGAC… sampl… SeuratPro… 127 56 0 A
## 5 AGTC… sampl… SeuratPro… 173 53 0 A
## 6 TCTG… sampl… SeuratPro… 70 48 0 A
## 7 TGGT… sampl… SeuratPro… 64 36 0 A
## 8 GCAG… sampl… SeuratPro… 72 45 0 A
## 9 GATA… sampl… SeuratPro… 52 36 0 A
## 10 AATG… sampl… SeuratPro… 100 41 0 A
## # ℹ 70 more rows
## # ℹ 11 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
## # ident <fct>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>,
## # tSNE_1 <dbl>, tSNE_2 <dbl>
Preliminary plots
Set colours and theme for plots.
# Use colourblind-friendly colours
friendly_cols <- dittoSeq::dittoColors()
# Set theme
custom_theme <-
list(
scale_fill_manual(values=friendly_cols),
scale_color_manual(values=friendly_cols),
theme_bw() +
theme(
panel.border=element_blank(),
axis.line=element_line(),
panel.grid.major=element_line(size=0.2),
panel.grid.minor=element_line(size=0.1),
text=element_text(size=12),
legend.position="bottom",
aspect.ratio=1,
strip.background=element_blank(),
axis.title.x=element_text(margin=margin(t=10, r=10, b=10, l=10)),
axis.title.y=element_text(margin=margin(t=10, r=10, b=10, l=10))
)
)
## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
We can treat pbmc_small_polished as a tibble for plotting.
Here we plot number of features per cell.
pbmc_small_polished |>
ggplot(aes(nFeature_RNA, fill=groups)) +
geom_histogram() +
custom_theme
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Here we plot total features per cell.
pbmc_small_polished |>
ggplot(aes(groups, nCount_RNA, fill=groups)) +
geom_boxplot(outlier.shape=NA) +
geom_jitter(width=0.1) +
custom_theme
Here we plot abundance of two features for each group.
pbmc_small_polished |>
join_features(features=c("HLA-DRA", "LYZ")) |>
ggplot(aes(groups, .abundance_counts + 1, fill=groups)) +
geom_boxplot(outlier.shape=NA) +
geom_jitter(aes(size=nCount_RNA), alpha=0.5, width=0.2) +
scale_y_log10() +
custom_theme
## tidySingleCellExperiment says: join_features produces duplicate cell names to accomadate the long data format. For this reason, a data frame is returned for independent data analysis. Assay feature abundance is appended as .abundance_counts and .abundance_logcounts.
Preprocess the dataset
We can also treat pbmc_small_polished as a SingleCellExperiment
object and proceed with data processing with Bioconductor packages, such
as scran [@lun2016pooling] and scater [@mccarthy2017scater].
# Identify variable genes with scran
variable_genes <-
pbmc_small_polished |>
modelGeneVar() |>
getTopHVGs(prop=0.1)
# Perform PCA with scater
pbmc_small_pca <-
pbmc_small_polished |>
runPCA(subset_row=variable_genes)
## Warning in check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - : more
## singular values/vectors requested than available
## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
## TRUE, : You're computing too large a percentage of total singular values, use a
## standard svd instead.
## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
## TRUE, : did not converge--results might be invalid!; try increasing work or
## maxit
pbmc_small_pca
## # A SingleCellExperiment-tibble abstraction: 80 × 18
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
## <chr> <fct> <dbl> <int> <fct> <fct> <chr>
## 1 ATGC… SeuratPro… 70 47 0 A g2
## 2 CATG… SeuratPro… 85 52 0 A g1
## 3 GAAC… SeuratPro… 87 50 1 B g2
## 4 TGAC… SeuratPro… 127 56 0 A g2
## 5 AGTC… SeuratPro… 173 53 0 A g2
## 6 TCTG… SeuratPro… 70 48 0 A g1
## 7 TGGT… SeuratPro… 64 36 0 A g1
## 8 GCAG… SeuratPro… 72 45 0 A g1
## 9 GATA… SeuratPro… 52 36 0 A g1
## 10 AATG… SeuratPro… 100 41 0 A g1
## # ℹ 70 more rows
## # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, sample <chr>,
## # ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>, PC5 <dbl>,
## # tSNE_1 <dbl>, tSNE_2 <dbl>
If a tidyverse-compatible package is not included in the
tidySingleCellExperiment collection, we can use as_tibble to
permanently convert tidySingleCellExperiment into a tibble.
# Create pairs plot with GGally
pbmc_small_pca |>
as_tibble() |>
select(contains("PC"), everything()) |>
GGally::ggpairs(columns=1:5, ggplot2::aes(colour=groups)) +
custom_theme
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
Identify clusters
We can proceed with cluster identification with scran.
pbmc_small_cluster <- pbmc_small_pca
# Assign clusters to the 'colLabels' of the SingleCellExperiment object
colLabels(pbmc_small_cluster) <-
pbmc_small_pca |>
buildSNNGraph(use.dimred="PCA") |>
igraph::cluster_walktrap() %$%
membership |>
as.factor()
## Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
## detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# Reorder columns
pbmc_small_cluster |> select(label, everything())
## # A SingleCellExperiment-tibble abstraction: 80 × 19
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## .cell label orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
## <chr> <fct> <fct> <dbl> <int> <fct> <fct>
## 1 ATGCC… 2 SeuratPro… 70 47 0 A
## 2 CATGG… 2 SeuratPro… 85 52 0 A
## 3 GAACC… 2 SeuratPro… 87 50 1 B
## 4 TGACT… 1 SeuratPro… 127 56 0 A
## 5 AGTCA… 2 SeuratPro… 173 53 0 A
## 6 TCTGA… 2 SeuratPro… 70 48 0 A
## 7 TGGTA… 1 SeuratPro… 64 36 0 A
## 8 GCAGC… 2 SeuratPro… 72 45 0 A
## 9 GATAT… 2 SeuratPro… 52 36 0 A
## 10 AATGT… 2 SeuratPro… 100 41 0 A
## # ℹ 70 more rows
## # ℹ 12 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
## # sample <chr>, ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>,
## # PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>
And interrogate the output as if it was a regular tibble.
# Count number of cells for each cluster per group
pbmc_small_cluster |>
count(groups, label)
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
## # A tibble: 8 × 3
## groups label n
## <chr> <fct> <int>
## 1 g1 1 12
## 2 g1 2 14
## 3 g1 3 14
## 4 g1 4 4
## 5 g2 1 10
## 6 g2 2 11
## 7 g2 3 10
## 8 g2 4 5
We can identify and visualise cluster markers combining SingleCellExperiment, tidyverse functions and tidyHeatmap [@mangiola2020tidyheatmap]
# Identify top 10 markers per cluster
marker_genes <-
pbmc_small_cluster |>
findMarkers(groups=pbmc_small_cluster$label) |>
as.list() |>
map(~ .x |>
head(10) |>
rownames()) |>
unlist()
# Plot heatmap
pbmc_small_cluster |>
join_features(features=marker_genes) |>
group_by(label) |>
heatmap(.feature, .cell, .abundance_counts, .scale="column")
## tidySingleCellExperiment says: join_features produces duplicate cell names to accomadate the long data format. For this reason, a data frame is returned for independent data analysis. Assay feature abundance is appended as .abundance_counts and .abundance_logcounts.
## tidyHeatmap says: (once per session) from release 1.7.0 the scaling is set to "none" by default. Please use scale = "row", "column" or "both" to apply scaling
## Warning: The `.scale` argument of `heatmap()` is deprecated as of tidyHeatmap 1.7.0.
## ℹ Please use scale (without dot prefix) instead: heatmap(scale = ...)
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
Reduce dimensions
We can calculate the first 3 UMAP dimensions using the SingleCellExperiment framework and scater.
pbmc_small_UMAP <-
pbmc_small_cluster |>
runUMAP(ncomponents=3)
And we can plot the result in 3D using plotly.
pbmc_small_UMAP |>
plot_ly(
x=~`UMAP1`,
y=~`UMAP2`,
z=~`UMAP3`,
color=~label,
colors=friendly_cols[1:4]
)
Cell type prediction
We can infer cell type identities using SingleR [@aran2019reference] and manipulate the output using tidyverse.
# Get cell type reference data
blueprint <- celldex::BlueprintEncodeData()
# Infer cell identities
cell_type_df <-
assays(pbmc_small_UMAP)$logcounts |>
Matrix::Matrix(sparse = TRUE) |>
SingleR::SingleR(
ref = blueprint,
labels = blueprint$label.main,
method = "single"
) |>
as.data.frame() |>
as_tibble(rownames="cell") |>
select(cell, first.labels)
# Join UMAP and cell type info
data(cell_type_df)
pbmc_small_cell_type <-
pbmc_small_UMAP |>
left_join(cell_type_df, by="cell")
## Warning in is_sample_feature_deprecated_used(x, .cols):
## tidySingleCellExperiment says: from version 1.3.1, the special columns
## including cell id (colnames(se)) has changed to ".cell". This dataset is
## returned with the old-style vocabulary (cell), however, we suggest to update
## your workflow to reflect the new vocabulary (.cell).
# Reorder columns
pbmc_small_cell_type |>
select(cell, first.labels, everything())
## Warning in is_sample_feature_deprecated_used(.data, .cols):
## tidySingleCellExperiment says: from version 1.3.1, the special columns
## including cell id (colnames(se)) has changed to ".cell". This dataset is
## returned with the old-style vocabulary (cell), however, we suggest to update
## your workflow to reflect the new vocabulary (.cell).
## # A SingleCellExperiment-tibble abstraction: 80 × 23
## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
## cell first.labels orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8
## <chr> <chr> <fct> <dbl> <int> <fct>
## 1 ATGCCAGAACGA… CD4+ T-cells SeuratPro… 70 47 0
## 2 CATGGCCTGTGC… CD8+ T-cells SeuratPro… 85 52 0
## 3 GAACCTGATGAA… CD8+ T-cells SeuratPro… 87 50 1
## 4 TGACTGGATTCT… CD4+ T-cells SeuratPro… 127 56 0
## 5 AGTCAGACTGCA… CD4+ T-cells SeuratPro… 173 53 0
## 6 TCTGATACACGT… CD4+ T-cells SeuratPro… 70 48 0
## 7 TGGTATCTAAAC… CD4+ T-cells SeuratPro… 64 36 0
## 8 GCAGCTCTGTTT… CD4+ T-cells SeuratPro… 72 45 0
## 9 GATATAACACGC… CD4+ T-cells SeuratPro… 52 36 0
## 10 AATGTTGACAGT… CD4+ T-cells SeuratPro… 100 41 0
## # ℹ 70 more rows
## # ℹ 17 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>,
## # file <chr>, sample <chr>, ident <fct>, label <fct>, PC1 <dbl>, PC2 <dbl>,
## # PC3 <dbl>, PC4 <dbl>, PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>, UMAP1 <dbl>,
## # UMAP2 <dbl>, UMAP3 <dbl>
We can easily summarise the results. For example, we can see how cell type classification overlaps with cluster classification.
# Count number of cells for each cell type per cluster
pbmc_small_cell_type |>
count(label, first.labels)
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
## # A tibble: 11 × 3
## label first.labels n
## <fct> <chr> <int>
## 1 1 CD4+ T-cells 2
## 2 1 CD8+ T-cells 8
## 3 1 NK cells 12
## 4 2 B-cells 10
## 5 2 CD4+ T-cells 6
## 6 2 CD8+ T-cells 2
## 7 2 Macrophages 1
## 8 2 Monocytes 6
## 9 3 Macrophages 1
## 10 3 Monocytes 23
## 11 4 Erythrocytes 9
We can easily reshape the data for building information-rich faceted plots.
pbmc_small_cell_type |>
# Reshape and add classifier column
pivot_longer(
cols=c(label, first.labels),
names_to="classifier", values_to="label"
) |>
# UMAP plots for cell type and cluster
ggplot(aes(UMAP1, UMAP2, color=label)) +
geom_point() +
facet_wrap(~classifier) +
custom_theme
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
We can easily plot gene correlation per cell category, adding multi-layer annotations.
pbmc_small_cell_type |>
# Add some mitochondrial abundance values
mutate(mitochondrial=rnorm(dplyr::n())) |>
# Plot correlation
join_features(features=c("CST3", "LYZ"), shape="wide") |>
ggplot(aes(CST3 + 1, LYZ + 1, color=groups, size=mitochondrial)) +
geom_point() +
facet_wrap(~first.labels, scales="free") +
scale_x_log10() +
scale_y_log10() +
custom_theme
## Warning in is_sample_feature_deprecated_used(x, .cols):
## tidySingleCellExperiment says: from version 1.3.1, the special columns
## including cell id (colnames(se)) has changed to ".cell". This dataset is
## returned with the old-style vocabulary (cell), however, we suggest to update
## your workflow to reflect the new vocabulary (.cell).
Nested analyses
A powerful tool we can use with tidySingleCellExperiment is tidyverse
nest. We can easily perform independent analyses on subsets of the
dataset. First we classify cell types into lymphoid and myeloid, and
then nest based on the new classification.
pbmc_small_nested <-
pbmc_small_cell_type |>
filter(first.labels != "Erythrocytes") |>
mutate(cell_class=dplyr::if_else(`first.labels` %in% c("Macrophages", "Monocytes"), "myeloid", "lymphoid")) |>
nest(data=-cell_class)
## Warning: There were 2 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `data = map(...)`.
## Caused by warning in `is_sample_feature_deprecated_used()`:
## ! tidySingleCellExperiment says: from version 1.3.1, the special columns including cell id (colnames(se)) has changed to ".cell". This dataset is returned with the old-style vocabulary (cell), however, we suggest to update your workflow to reflect the new vocabulary (.cell).
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.
pbmc_small_nested
## # A tibble: 2 × 2
## cell_class data
## <chr> <list>
## 1 lymphoid <SnglCllE[,40]>
## 2 myeloid <SnglCllE[,31]>
Now we can independently for the lymphoid and myeloid subsets (i) find variable features, (ii) reduce dimensions, and (iii) cluster using both tidyverse and SingleCellExperiment seamlessly.
pbmc_small_nested_reanalysed <-
pbmc_small_nested |>
mutate(data=map(
data, ~ {
.x <- runPCA(.x, subset_row=variable_genes)
variable_genes <-
.x |>
modelGeneVar() |>
getTopHVGs(prop=0.3)
colLabels(.x) <-
.x |>
buildSNNGraph(use.dimred="PCA") |>
igraph::cluster_walktrap() %$%
membership |>
as.factor()
.x |> runUMAP(ncomponents=3)
}
))
pbmc_small_nested_reanalysed
## # A tibble: 2 × 2
## cell_class data
## <chr> <list>
## 1 lymphoid <SnglCllE[,40]>
## 2 myeloid <SnglCllE[,31]>
We can then unnest and plot the new classification.
pbmc_small_nested_reanalysed |>
# Convert to tibble otherwise SingleCellExperiment drops reduced dimensions when unifying data sets.
mutate(data=map(data, ~ .x |> as_tibble())) |>
unnest(data) |>
# Define unique clusters
unite("cluster", c(cell_class, label), remove=FALSE) |>
# Plotting
ggplot(aes(UMAP1, UMAP2, color=cluster)) +
geom_point() +
facet_wrap(~cell_class) +
custom_theme
We can perform a large number of functional analyses on data subsets. For example, we can identify intra-sample cell-cell interactions using SingleCellSignalR [@cabello2020singlecellsignalr], and then compare whether interactions are stronger or weaker across conditions. The code below demonstrates how this analysis could be performed. It won’t work with this small example dataset as we have just two samples (one for each condition). But some example output is shown below and you can imagine how you can use tidyverse on the output to perform t-tests and visualisation.
pbmc_small_nested_interactions <-
pbmc_small_nested_reanalysed |>
# Unnest based on cell category
unnest(data) |>
# Create unambiguous clusters
mutate(integrated_clusters=first.labels |> as.factor() |> as.integer()) |>
# Nest based on sample
nest(data=-sample) |>
mutate(interactions=map(data, ~ {
# Produce variables. Yuck!
cluster <- colData(.x)$integrated_clusters
data <- data.frame(assays(.x) |> as.list() |> extract2(1) |> as.matrix())
# Ligand/Receptor analysis using SingleCellSignalR
data |>
cell_signaling(genes=rownames(data), cluster=cluster) |>
inter_network(data=data, signal=_, genes=rownames(data), cluster=cluster) %$%
`individual-networks` |>
map_dfr(~ bind_rows(as_tibble(.x)))
}))
pbmc_small_nested_interactions |>
select(-data) |>
unnest(interactions)
If the dataset was not so small, and interactions could be identified, you would see something like below.
data(pbmc_small_nested_interactions)
pbmc_small_nested_interactions
## # A tibble: 100 × 9
## sample ligand receptor ligand.name receptor.name origin destination
## <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 sample1 cluster 1.PTMA cluster… PTMA VIPR1 clust… cluster 2
## 2 sample1 cluster 1.B2M cluster… B2M KLRD1 clust… cluster 2
## 3 sample1 cluster 1.IL16 cluster… IL16 CD4 clust… cluster 2
## 4 sample1 cluster 1.HLA-B cluster… HLA-B KLRD1 clust… cluster 2
## 5 sample1 cluster 1.CALM1 cluster… CALM1 VIPR1 clust… cluster 2
## 6 sample1 cluster 1.HLA-E cluster… HLA-E KLRD1 clust… cluster 2
## 7 sample1 cluster 1.GNAS cluster… GNAS VIPR1 clust… cluster 2
## 8 sample1 cluster 1.B2M cluster… B2M HFE clust… cluster 2
## 9 sample1 cluster 1.PTMA cluster… PTMA VIPR1 clust… cluster 3
## 10 sample1 cluster 1.CALM1 cluster… CALM1 VIPR1 clust… cluster 3
## # ℹ 90 more rows
## # ℹ 2 more variables: interaction.type <chr>, LRscore <dbl>
Aggregating cells
Sometimes, it is necessary to aggregate the gene-transcript abundance from a group of cells into a single value. For example, when comparing groups of cells across different samples with fixed-effect models.
In tidySingleCellExperiment, cell aggregation can be achieved using the
aggregate_cells function.
pbmc_small |>
aggregate_cells(groups, assays = "counts")
## class: SummarizedExperiment
## dim: 230 2
## metadata(0):
## assays(1): counts
## rownames(230): ACAP1 ACRBP ... ZNF330 ZNF76
## rowData names(0):
## colnames(2): g1 g2
## colData names(4): .aggregated_cells groups orig.ident file
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