Clustering at k60

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

Annotation

We make a first rough annotation using known markers for different celltypes.

Click to expand the Neurons marker plots 

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

Click to expand the Stromal marker plots 

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

Click to expand the Epithelial cells 

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

Click to expand the Astrocytes marker plots 

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

Click to expand the Immune cells plots 

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

Click to expand the Oligodendroglia marker plots 

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.

Click to expand the ependymal marker plots

Generate marker list

We compute here a pairwise differential expression between all the clusters. The results are saved in a list of dataframes, one for each cluster.

Rename the Clusters with assigned Cell Types

For this first annotation we will rename the levels from the k=60 clustering as follows:

1 Microglia-Macrophages

2 Endothelial-Pericytes

3 Astrocytes

4 OPC

5 Immune

6 Astrocytes

7 Monocytes

8 Astrocytes

9 Oligo

10 Neuron?

11 Chp-epithelial

12 Oligo

13 NA

14 Oligo

15 Neuron

16 Microglia-Macrophages-BAM

17 Oligo?

18 Oligo

19 OPC

20 Endothelial-Pericytes

21 Microglia-Macrophages

22 Endothelial-Pericytes

23 Astrocytes

24 Microglia-Macrophages

## Scale for 'colour' is already present. Adding another scale for 'colour',
## which will replace the existing scale.