Seurat: Plot order VlnPlot

[balthasar0810]

Dear all,

this is maybe a trivial question but how can I provide the exact sample order in VlnPlots?

Thanks and sorry, Christian

[leonfodoulian]

Hi,

You can simply set an order of cluster identities as follows:

# Define an order of cluster identities
my_levels <- c(4,3,2,1)

# Relevel object@ident
object@ident <- factor(x = object@ident, levels = my_levels)

Best,
Leon

[balthasar0810]

Thanks, Leon!

---

Dr. med Dipl.-Math. Christian Hinze

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Max-Delbrück-Centrum
für Molekulare Medizin (MDC) Berlin-Buch
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Tel.: [phone]
christian.[email protected]

Medizinische Klinik mit Schwerpunkt Nephrologie
Charité - Universitätsmedizin Berlin
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Tel. [phone]
christian.[email protected][e-mail]

---

Von: Leon Fodoulian [[email protected]]
Gesendet: Mittwoch, 2. Mai 2018 19:55
An: satijalab/seurat
Cc: balthasar0810; Author
Betreff: [ext] Re: [satijalab/seurat] Plot order VlnPlot (#454)

Hi,

You can simply set an order of cluster identities as follows:

Define an order of cluster identities

my_levels <- c(4,3,2,1)

Relevel object@ident

object@ident <- factor(x = object@ident, levels = my_levels)

Best,
Leon

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[leonfodoulian]

Could you please close this issue?

Thank you!
Leon

[Frankshi5011]

Hello: I am new to Seurat. How do I do this in Seurat 3? The method described above does work.
Thanks
Frank

[Landbruce]

Hello everyone, I am struggling to change the order of my clusters in the graphs using seurat v3.0.
I ordered them using the ClusterTree function but they came out in descending way to what I want for my graphs. I.e (*4,3,2,1) instead of (1,2,3,4). How can use the version3 to reorder the clusters list?
I have been trying the suggestions above and they are not working. Thank you so much. Victor

[tmccra2]

I am also wondering how to apply this to version 3.

Thanks!

[AndyR2]

This works for me in S v3.

object_copy <- object
my_levels <- c(set_custom_order_of_clusters)
Idents(object_copy) <- factor(Idents(object_copy), levels= my_levels)

VlnPlot(object_copy, features = c("some_gene"))

study the command changes here [under tab S v2.x vs S v3.X] to transition from v2 to v3
https://satijalab.org/seurat/essential_commands.html