Testis 3 Individual Clustering

UNDER CONSTRUCTION

Testis 3 Individual Clustering

Normalize Data

sobj <- FindVariableFeatures(
    sobj,
    selection.method = "vst",
    nfeatures = 2000,
    verbose = FALSE
)

top20 <- head(VariableFeatures(sobj), 20)

Scale Data

all_genes <- rownames(sobj)

sobj <- ScaleData(
    sobj,
    features = all_genes,
    vars.to.regress = "nCount_RNA",
    verbose = FALSE
)

Dimensionality Reduction

Dimensional Gene Loadings

Top Genes Heatmap

JackStraw

Elbow Plot

Dimension Selection

Clustering

ResolutionNum of Clusters
0.411
0.513
0.613
0.715
0.816
0.917
119
1.118
1.221

Look at marker genes

Spermatogonia

Spermatocytes

CySC

TE

PC

hub

Cluster Markers

clusterNum Biomarkers per Cluster
0160
1786
2567
3344
465
51,486
6453
71,355
8844
9801
10364
111,002
121,390