2 Cell type annotation

2.1 Manual annotation

Please refer to the Cell cluster annotation session.

2.2 Automatic annotation

2.2.1 Run SingleR

library(SingleR)

hpca <- celldex::HumanPrimaryCellAtlasData()
hpca

## class: SummarizedExperiment 
## dim: 19363 713 
## metadata(0):
## assays(1): logcounts
## rownames(19363): A1BG A1BG-AS1 ... ZZEF1 ZZZ3
## rowData names(0):
## colnames(713): GSM112490 GSM112491 ... GSM92233
##   GSM92234
## colData names(3): label.main label.fine label.ont

res <- SingleR(test = assay(pbmc, "logcounts"), ref = hpca, labels = hpca$label.main)
head(res)

## DataFrame with 6 rows and 4 columns
##                            scores      labels delta.next
##                          <matrix> <character>  <numeric>
## 1 0.1040907:0.233575:0.222844:...     T_cells  0.0888618
## 2 0.1017499:0.358524:0.299235:...      B_cell  0.3046119
## 3 0.0696533:0.265561:0.237793:...     T_cells  0.1985708
## 4 0.0863639:0.235842:0.275857:...    Monocyte  0.0503585
## 5 0.0737555:0.164465:0.175442:...     NK_cell  0.0892196
## 6 0.1281878:0.258801:0.249245:...     T_cells  0.0775251
##   pruned.labels
##     <character>
## 1       T_cells
## 2        B_cell
## 3       T_cells
## 4      Monocyte
## 5       NK_cell
## 6       T_cells

dice <- celldex::DatabaseImmuneCellExpressionData()
res2 <- SingleR(test = assay(pbmc, "logcounts"), ref = dice, labels = dice$label.main)
head(res2)

## DataFrame with 6 rows and 4 columns
##                                scores        labels
##                              <matrix>   <character>
## 1  0.01278759:0.0594162:0.1731098:... T cells, CD4+
## 2  0.26468267:0.1424061:0.0667195:...       B cells
## 3  0.03184648:0.0768767:0.2039776:... T cells, CD4+
## 4 -0.00914745:0.3439882:0.0610696:...     Monocytes
## 5 -0.04285154:0.0396558:0.2513840:...      NK cells
## 6  0.06123675:0.0980547:0.1470082:... T cells, CD4+
##   delta.next pruned.labels
##    <numeric>   <character>
## 1 0.00808206 T cells, CD4+
## 2 0.12227658       B cells
## 3 0.05825145 T cells, CD4+
## 4 0.28291862     Monocytes
## 5 0.15577995      NK cells
## 6 0.12673642 T cells, CD4+

2.2.2 Annotate with SingleR result

pbmc[['hpca_label']] <- res$labels

pbmc[['dice_label']] <- res2$labels

2.2.3 Comparision with manual annotation result

x <- colData(pbmc)[, c("label", "hpca_label", "dice_label")]

plot_list(
    manual = sc_dim(pbmc, reduction="UMAP"),    
    hpca = sc_dim(pbmc, reduction="UMAP", mapping=aes(color=hpca_label)),
    dice = sc_dim(pbmc, reduction="UMAP", mapping=aes(color=dice_label)),
    ncol = 3) & 
sc_dim_geom_label(geom = ggrepel::geom_text_repel) & 
theme(legend.position='inside')

table(x[,c(1,2)])

##                hpca_label
## label           B_cell CMP Monocyte NK_cell Platelets
##   CD8+ T             0   0        0      32         0
##   B                333   2        0       0         0
##   Memory CD4+        0   0        0       0         0
##   CD14+ Mono         0   0      444       0         0
##   NK                 0   0        0     155         0
##   FCGR3A+ Mono       0   0      152       0         0
##   Native CD4+ T      0   2        0       2         0
##   DC                 0   0       19       0         0
##   Platelet           0   0        0       0        12
##                hpca_label
## label           Pre-B_cell_CD34- Pro-B_cell_CD34+ T_cells
##   CD8+ T                       1                1     363
##   B                            3                4       7
##   Memory CD4+                  2                0     529
##   CD14+ Mono                  48                0       0
##   NK                           1                0       1
##   FCGR3A+ Mono                 6                0       1
##   Native CD4+ T                2                0     514
##   DC                           2                0       0
##   Platelet                     0                0       0

table(x[,c(1,3)])

##                dice_label
## label           B cells Monocytes NK cells T cells, CD4+
##   CD8+ T              0         1      174           148
##   B                 340         4        1             3
##   Memory CD4+         0         0        0           495
##   CD14+ Mono          0       492        0             0
##   NK                  0         0      157             0
##   FCGR3A+ Mono        0       159        0             0
##   Native CD4+ T       0         2        0           279
##   DC                  0        21        0             0
##   Platelet            0        12        0             0
##                dice_label
## label           T cells, CD8+
##   CD8+ T                   74
##   B                         1
##   Memory CD4+              36
##   CD14+ Mono                0
##   NK                        0
##   FCGR3A+ Mono              0
##   Native CD4+ T           239
##   DC                        0
##   Platelet                  0