Error while simulating spot-resolution spatial data for cell-type deconvolution

SONGDONGYUAN1994 / scDesign3

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

https://songdongyuan1994.github.io/scDesign3/docs/index.html

MIT License

81 stars 23 forks source link

Error while simulating spot-resolution spatial data for cell-type deconvolution #9

Closed sumeer1 closed 1 year ago

sumeer1 commented 1 year ago

Hi,

I am trying to run the tutorial for simulating spot-resolution spatial data for cell-type deconvolution but I am getting error while running this block of code:

Error: Error in xtfrm.data.frame(x) : cannot xtfrm data frames

MOBSP_data <- construct_data(
  sce = MOBSP_sce,
  assay_use = "counts",
  celltype = NULL,
  pseudotime = NULL,
  spatial = c("spatial1", "spatial2"),
  other_covariates = NULL,
  corr_by = "1"
)

qw130 commented 1 year ago

Hi Sumeer,

Thanks for your interest in our work and for pointing out this issue! I pushed the fixed code and now you should be able to run the tutorial for simulating spot-resolution spatial data for cell-type deconvolution with no issue.

Best, Qingyang