Can't utilize plot_cpdb3,4 functions using my data
cacaonib opened this issue · 4 comments
Hi Thanks for making a good package
I tried to use plot_cpdb3 and plot_cpdb4 for chord plot
I got the Error
p <- plot_cpdb3(cell_type1 = 'T cells', cell_type2 = 'B cells',
scdata = sce,
idents = 'cell_type', # column name where the cell ids are located in the metadata
means = means,
pvals = pvals,
deconvoluted = decon, # new options from here on specific to plot_cpdb3
keep_significant_only = TRUE,
standard_scale = TRUE,
remove_self = TRUE
)
Error in plot_cpdb3(cell_type1 = "T cells", cell_type2 = "B cells", scdata = sce, :
Sorry not supported. Please use a SingleCellExperiment object.
So, I try the same function using "kidneyimmune data" (practice data)
this data can draw chord plot
so this error means, now I can not use my data in plot_cpdb3 and plot_cpdb3?
Thanks
Hi, @cacaonib. I'm guessing you are using a Seurat
object. Please convert to SingleCellExperiment
first. you can use Seurat's as.SingleCellExperiment
to do that.
Hi, @cacaonib. I'm guessing you are using a
Seurat
object. Please convert toSingleCellExperiment
first. you can use Seurat'sas.SingleCellExperiment
to do that.
OH...Sorry
I missed the simple thing.
Thanks for the quick answer!!
Have a good day!!
no worries! let me know if there's other issues.
no worries! let me know if there's other issues.
No.
Now, this functions work pretty well