Timeline for How to set the position of groups in a Seurat object on a FeatureHeatmap plot
Current License: CC BY-SA 4.0
8 events
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| Jan 21, 2019 at 14:33 | comment | added | TimStuart |
Can you confirm Seurat v3 has actually been installed and loaded before running UpdateSeuratObject?
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| Jan 20, 2019 at 15:11 | comment | added | Charles |
I obtain this: devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0') : package ‘curl’ successfully unpacked and MD5 sums checked: Error: (converted from warning) cannot remove prior installation of package ‘curl’. UpdateSeuratObject(object): Object representation is consistent with the most current Seurat version. The FeatureHeatmap() actually uses the alphabetical order of the conditions which I provided in the metadata slot. Is there a possibility to reorder the factor levels without harming the integrity of the data in the Seurat object?
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| Jan 18, 2019 at 16:30 | comment | added | TimStuart |
You can install v3 using devtools: devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0'). I don't know how much effort it is for you to repeat analyses with Seurat v3, but you can also just update the Seurat object using UpdateSeuratObject. See here for more information: satijalab.org/seurat/essential_commands.html
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| Jan 18, 2019 at 15:36 | comment | added | Charles | Will it also be advisable that I move to Seurat V3 at this level or I may need to restart my analyses afresh and repeat all steps with Seurat V3? | |
| Jan 18, 2019 at 15:34 | comment | added | Charles | How do I get the Seurat V3 package? My computer is having issue downloading it automaticaally, so I wish to download the Seurat V3 package manually and then load it. Thanks. @TimStuart | |
| Jan 18, 2019 at 14:37 | comment | added | TimStuart | Yes, that function is part of Seurat v3. This answer will only work for v3 | |
| Jan 18, 2019 at 14:26 | comment | added | Charles |
Thanks a lot. However the function VariableFeatures is not present in my Seurat package. I get the error: Error in VariableFeatures(object) : could not find function "VariableFeatures" @TimStuart
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| Jan 18, 2019 at 14:04 | history | answered | TimStuart | CC BY-SA 4.0 |