Testis 2 Individual Clustering

UNDER CONSTRUCTION

Testis 2 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
0.410
0.512
0.614
0.715
0.816
0.917
118
1.120
1.220

Look at marker genes

Spermatogonia

Spermatocytes

CySC

TE

PC

hub

Cluster Markers

clusterNum Biomarkers per Cluster
0359
1392
2683
31,375
4556
5377
61,615
7501
81,088
91,918
10286
11570
121,933
1374