Clustering QC - Answer Key

Author

Will Gammerdinger

Published

July 1, 2025

Exercise 1

Hypothesize the clusters corresponding to each of the different clusters in the table:

Cell Type	Clusters
CD14+ monocytes	1, 3
FCGR3A+ monocytes	10
Conventional dendritic cells	14
Plasmacytoid dendritic cells	16
Marcrophages	-
B cells	?
T cells	?
CD4+ T cells	?
CD8+ T cells	?
NK cells	?
Megakaryocytes	?
Erythrocytes	?
Unknown	?

B Cells

FeaturePlot(seurat_integrated, 
            reduction = "umap", 
            features = c("CD79A", "MS4A1"), 
            order = TRUE,
            min.cutoff = 'q10', 
            label = TRUE)

B cells appear to be clusters 7, 11 and 13.

T cells

FeaturePlot(seurat_integrated, 
            reduction = "umap", 
            features = c("CD3D"), 
            order = TRUE,
            min.cutoff = 'q10', 
            label = TRUE)

T cells appear to be clusters 0, 2, 4, 5, 6 and 9.

CD4+ T cells

FeaturePlot(seurat_integrated, 
            reduction = "umap", 
            features = c("CD3D", "IL7R", "CCR7"), 
            order = TRUE,
            min.cutoff = 'q10', 
            label = TRUE)

CD4+ T cells appear to be clusters 0, 2, 4 and 6.

CD8+ T cells

FeaturePlot(seurat_integrated, 
            reduction = "umap", 
            features = c("CD3D", "CD8A"), 
            order = TRUE,
            min.cutoff = 'q10', 
            label = TRUE)

CD8+ T cells appear to be clusters 5 and 9.

NK cells

FeaturePlot(seurat_integrated, 
            reduction = "umap", 
            features = c("GNLY", "NKG7"), 
            order = TRUE,
            min.cutoff = 'q10', 
            label = TRUE)

NK cells appear to be clusters 8 and 12.

Megakaryocytes

FeaturePlot(seurat_integrated, 
            reduction = "umap", 
            features = c("PPBP"), 
            order = TRUE,
            min.cutoff = 'q10', 
            label = TRUE)

Megakaryocytes appear to be clusters 15.

Erythrocytes

FeaturePlot(seurat_integrated, 
            reduction = "umap", 
            features = c("HBB", "HBA2"), 
            order = TRUE,
            min.cutoff = 'q10', 
            label = TRUE)

Erythrocytes don’t appear to be present.

Cell Type	Clusters
CD14+ monocytes	1, 3
FCGR3A+ monocytes	10
Conventional dendritic cells	14
Plasmacytoid dendritic cells	16
Marcrophages	-
B cells	7, 11, 13
T cells	0, 2, 4, 5, 6, 9
CD4+ T cells	0, 2, 4, 6
CD8+ T cells	5, 9
NK cells	8, 12
Megakaryocytes	15
Erythrocytes	-

--- title: "Clustering QC - Answer Key" author: "Will Gammerdinger" date: "Tuesday, July 1, 2025" --- ```{r} #| label: load_libraries #| echo: false library(Seurat) library(tidyverse) library(ggplot2) library(cowplot) load(bzfile("data/additional_data/seurat_integrated.RData.bz2")) ``` # Exercise 1 Hypothesize the clusters corresponding to each of the different clusters in the table: | Cell Type | Clusters | |:---:|:---:| | CD14+ monocytes | 1, 3 | | FCGR3A+ monocytes | 10 | | Conventional dendritic cells | 14 | | Plasmacytoid dendritic cells | 16 | | Marcrophages | - | | B cells | ? | | T cells | ? | | CD4+ T cells | ? | | CD8+ T cells| ? | | NK cells | ? | | Megakaryocytes | ? | | Erythrocytes | ? | | Unknown | ? | ## B Cells ```{r} #| label: B_cells_plot FeaturePlot(seurat_integrated, reduction = "umap", features = c("CD79A", "MS4A1"), order = TRUE, min.cutoff = 'q10', label = TRUE) ``` B cells appear to be clusters 7, 11 and 13. ## T cells ```{r} #| label: T_cells_plot FeaturePlot(seurat_integrated, reduction = "umap", features = c("CD3D"), order = TRUE, min.cutoff = 'q10', label = TRUE) ``` T cells appear to be clusters 0, 2, 4, 5, 6 and 9. ## CD4+ T cells ```{r} #| label: CD4_T_cells_plot FeaturePlot(seurat_integrated, reduction = "umap", features = c("CD3D", "IL7R", "CCR7"), order = TRUE, min.cutoff = 'q10', label = TRUE) ``` CD4+ T cells appear to be clusters 0, 2, 4 and 6. ## CD8+ T cells ```{r} #| label: CD8_T_cells_plot FeaturePlot(seurat_integrated, reduction = "umap", features = c("CD3D", "CD8A"), order = TRUE, min.cutoff = 'q10', label = TRUE) ``` CD8+ T cells appear to be clusters 5 and 9. ## NK cells ```{r} #| label: NK_cells_plot FeaturePlot(seurat_integrated, reduction = "umap", features = c("GNLY", "NKG7"), order = TRUE, min.cutoff = 'q10', label = TRUE) ``` NK cells appear to be clusters 8 and 12. ## Megakaryocytes ```{r} #| label: Megakaryocytes_plot FeaturePlot(seurat_integrated, reduction = "umap", features = c("PPBP"), order = TRUE, min.cutoff = 'q10', label = TRUE) ``` Megakaryocytes appear to be clusters 15. ## Erythrocytes ```{r} #| label: Erythrocytes_plot FeaturePlot(seurat_integrated, reduction = "umap", features = c("HBB", "HBA2"), order = TRUE, min.cutoff = 'q10', label = TRUE) ``` Erythrocytes don't appear to be present. *** | Cell Type | Clusters | |:---:|:---:| | CD14+ monocytes | 1, 3 | | FCGR3A+ monocytes | 10 | | Conventional dendritic cells | 14 | | Plasmacytoid dendritic cells | 16 | | Marcrophages | - | | B cells | 7, 11, 13 | | T cells | 0, 2, 4, 5, 6, 9 | | CD4+ T cells | 0, 2, 4, 6 | | CD8+ T cells| 5, 9 | | NK cells | 8, 12 | | Megakaryocytes | 15 | | Erythrocytes | - |