search

Ginnay / DcjComm

Cell clustering and communication network inference for single-cell transcriptomics
GNU General Public License v3.0
11 stars 0 forks source link

Request for method to convert Seurat object to DcjComm input format #7

Open songsong711 opened 1 month ago

songsong711 commented 1 month ago

Hello DcjComm developers,

First, thank you for your excellent work on the DcjComm package!

I am currently working on a project using Seurat to analyze single-cell RNA-seq data, and I would like to use DcjComm for further analysis. However, I am having trouble figuring out how to convert a Seurat object into the necessary input formats required by DcjComm, specifically:

lst_scrna cell_group true_labs W Could you kindly provide some guidance or an example on how to extract or transform data from a Seurat object to generate these files? Any code examples, documentation, or tips would be greatly appreciated.

Thank you for your time and help!

23461044xc commented 1 month ago

I encountered the same problem.

aotai12138 commented 1 month ago 
g <- ggplot(fdata, aes(x = tfscore , y = fenzu , fill = fenzu)) +
  geom_density_ridges_gradient(scale=3) +
  theme_ridges() +
  xlab(NULL) + ylab(NULL) + DOSE::theme_dose() +
  theme(text = element_text(
    size = 10, face = "bold", color = "black", family = "Times")) + theme_bw() +
  theme(axis.title.x = element_text(size = 10, face = "bold", color = "black"),
        axis.title.y = element_text(size = 10, face = "bold", color = "black"),
        axis.text.y = element_text(size = 9, face = "bold", color = "black"),
        axis.text.x = element_text(size = 9, face = "bold", color = "black"))

I encountered the same issue.

Additionally, in the above example code, fdata does not generate tfscore and fenzu. How are these mapped values obtained?

Thank you for your time and help!