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 AG Schmidt-Ott Max-Delbrück-Centrum für Molekulare Medizin (MDC) Berlin-Buch Robert-Rössle-Str. 10 13125 Berlin Tel.: +49 30 9406 3240 christian.hinze@mdc-berlin.de Medizinische Klinik mit Schwerpunkt Nephrologie Charité - Universitätsmedizin Berlin Campus Benjamin Franklin Hindenburgdamm 30 12203 Berlin Tel. +49 30 8445 2441 christian.hinze@charite.de<mailto:kai.schmidt-ott@charite.de>

________________________________ Von: Leon Fodoulian [notifications@github.com] 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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#454 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AJwpDB_rc2gx1PBdV95MPfz91sk3Qyd7ks5tufMHgaJpZM4Tvyn0>.

[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