Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Keep original name from Panglao when creating consensus reference #976

Conversation

allyhawkins
Copy link
Member

I was working on #969 and I noticed that we don't actually keep the original name used in the cell type assignment from Panglao/CellAssign when we create the reference table for consensus labels. We were only saving the cell ontology ID and the name in the cell ontology. This means we can't actually join that table with the colData for ScPCA samples since there won't be a column that matches.

At first I thought we could just use the table that we made that maps each name from Panglao to the cell ontology ID, but there are cases where we have multiple ontology IDs that map to different Panglao assignments. So here I'm adding in a column to the consensus cell types and adding a few more rows to the reference that account for cases where the same ontology ID maps to different names in Panglao.

@allyhawkins
Copy link
Member Author

For reference these are the new lines:

CL:0000576	monocyte	Osteoclast precursor cells	CL:0000775	Neutrophils	Neutrophils	CL:0000766	myeloid leukocyte
CL:0000576	monocyte	Osteoclast precursor cells	CL:0000576	Monocytes	Monocytes	CL:0000576	monocyte
CL:0000576	monocyte	Monocytes	CL:0000451	DC	DC	CL:0000113	mononuclear phagocyte
CL:0000576	monocyte	Osteoclast precursor cells	CL:0000771	Eosinophils	Eosinophils	CL:0000766	myeloid leukocyte
CL:0000746	cardiac muscle cell	Cardiomyocytes	CL:0000192	Smooth muscle	Smooth muscle	CL:0000187	muscle cell
CL:0000359	vascular associated smooth muscle cell	Vascular smooth muscle cells	CL:0000192	Smooth muscle	Smooth muscle	CL:0000192	smooth muscle cell
CL:0000746	cardiac muscle cell	Cardiomyocytes	CL:0000187	Myocytes	Myocytes	CL:0000187	muscle cell
CL:0000359	vascular associated smooth muscle cell	Pulmonary vascular smooth muscle cells	CL:0000187	Myocytes	Myocytes	CL:0000187	muscle cell
CL:0000359	vascular associated smooth muscle cell	Vascular smooth muscle cells	CL:0000187	Myocytes	Myocytes	CL:0000187	muscle cell
CL:0002573	Schwann cell	Peri-islet Schwann cells	CL:0000127	Astrocytes	Astrocytes	CL:0000125	glial cell

Copy link
Member

@jaclyn-taroni jaclyn-taroni left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

👍🏻

@allyhawkins allyhawkins merged commit 9315b5a into AlexsLemonade:main Jan 8, 2025
3 checks passed
@allyhawkins allyhawkins deleted the allyhawkins/add-original-panglao-name branch January 8, 2025 19:08
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants