Closed Dazcam closed 3 years ago
Thank you, Darren. This is actually my task this week (well timed question!) so I would expect a fix quite soon.
Best, Erica
Hi Erica,
Thank you for the quick response. Excited to hear you will be incorporating Seurat 4 updates soon. If you can, please drop me a line if/when you manage to post the updated code.
Best,
Darren
Hi Darren,
I have now updated DoubletDecon and it should work with Seurat 4. The changes I made:
As for the error "Error in plot.new() : figure margins too large", I have seen this most frequently with users of R Studio. THe plot that is trying to generate is too big for the size of the plot window you have allotted in the UI of R Studio. To correct this, just drag the plot window a little wider and taller and see if that fixes it. Source: https://stackoverflow.com/questions/12766166/error-in-plot-new-figure-margins-too-large-in-r. If you are not using R Studio or if this doesn't solve the problem, please reach back out in a new issue and I will try to help fix it.
I tested both Seurat 3.2.2 and Seurat 3.9.9 (v4) using 2 different objects on 2 machines, but please let me know if you catch something else while using DoubletDecon. Bugs appear sometimes despite careful testing! Thanks for bringing this up, hope you enjoy!
Best, Erica
Confirmation:
packageVersion("Seurat") [1] ‘3.2.2’
extract marker genes
seuratObject.markers=FindAllMarkers(object = seuratObject, only.pos = TRUE, min.pct=0.25) Calculating cluster 0 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=03s
Calculating cluster 1 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02s
Calculating cluster 2 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=04s
Calculating cluster 3 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s
head(seuratObject.markers) p_val avg_logFC pct.1 pct.2 p_val_adj cluster gene UG0898H09 2.193383e-17 186.18414 0.934 0.642 5.195247e-13 0 UG0898H09 NPFFR2 5.595162e-16 165.79417 0.934 0.563 1.325270e-11 0 NPFFR2 ZFAT 8.933254e-15 35.57417 0.669 0.333 2.115931e-10 0 ZFAT KIF18B 1.604839e-14 Inf 1.000 0.777 3.801221e-10 0 KIF18B PDE4C 2.821303e-14 72.87417 1.000 0.807 6.682538e-10 0 PDE4C ST8SIA1 3.512976e-14 96.62416 0.967 0.682 8.320835e-10 0 ST8SIA1packageVersion("Seurat") [1] ‘3.9.9.9010’
extract marker genes
seuratObject.markers=FindAllMarkers(object = seuratObject, only.pos = TRUE, min.pct=0.25) Calculating cluster 0 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02s
Calculating cluster 1 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02s
Calculating cluster 2 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=04s
Calculating cluster 3 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s
head(seuratObject.markers) p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene UG0898H09 2.193383e-17 268.60693 0.934 0.642 5.195247e-13 0 UG0898H09 NPFFR2 5.595162e-16 239.19043 0.934 0.563 1.325270e-11 0 NPFFR2 ZFAT 8.933254e-15 51.32268 0.669 0.333 2.115931e-10 0 ZFAT KIF18B 1.604839e-14 Inf 1.000 0.777 3.801221e-10 0 KIF18B PDE4C 2.821303e-14 105.13520 1.000 0.807 6.682538e-10 0 PDE4C ST8SIA1 3.512976e-14 139.39920 0.967 0.682 8.320835e-10 0 ST8SIA1
Many Thanks for the update Erica.
I will have a go at running this today, and thanks for the link regarding the plotting issue. I am using R studio so this is almost certainly the cause.
Best,
Darren
Hi there,
I'm looking to run Doublet Decon using Seurat 4 but after following the instructions on your wiki I get some errors.
The first couple I could 'fix' as they appeared to relate to the changes the developers of Seurat 4 made to the the fold change parameters of the FindMarkers() function:
These updates affected two lines (lines 20-21) of the code in the
Improved_Seurat_Pre_Process()
function.However, the after running
Improved_Seurat_Pre_Process()
andMain_Doublet_Decon()
I get the following error:I noticed that in
Improved_Seurat_Pre_Process()
code the lineexpression=as.data.frame(seuratObject@assays[["RNA"]]@counts)
points to the raw counts in my data whereas the normalised counts are actually stored inseuratObject@assays[["RNA"]]@data
. As the example file in your wiki shows normalised counts I tried both@counts
and@data
but got the same error.Are you considering updating Doublet Decon to incorporate data generated by Seurat 4? If so, I can send more details regarding these issues.
Best Wishes,
Darren