marcelosua / spotlight_deconvolution_analysis Goto Github PK

Hi @MarcElosua,

Thank you for the SPOTlight package and this code here to reproduce the results of your paper. I am just wondering whether you are planning to make a public repository (e.g. on zenodo) where you will put the Seurat objects of the processed spatial data (or the spatial data you load in your 'pancreas_PDAC/0-inDrop_itai_annotation.Rmd' script). I started looking at the PDAC data downloaded from GEO myself but it seems to take some time and work to convert it to the right format to run the analyses you show here. Therefore I thought I could just ask whether it would be possible to share the PDAC Seurat objects after processing (or the direct and concrete input data of that script) .

Thank you in advance!

Hi Marc,

Your SPOTlight package is pretty awesome. I have a little question about the code. In common_synthetic_spots.Rmd, there is a line of code, "source(here::here("misc/paths_vrs.R"))". But I couldn't find the folder "misc". Could you give me some help and explain the code?

Thank you a lot!

BW

Yu

Hi,
It's a good work about your method.
You could provid the data about processed Mus Musculus Brain ST.rds and SC.rds ?

Hi @MarcElosua,

Thank you for you nice work SPOTlight!

From GSE111672, I can not find annotations for scRNA-seq data, and detailed data (e.g., filtered_feature_bc_matrix.tsv, tissue_positions_list_spatial_object.tsv, lowres_rot.jpg) for ST.

For example, when I tried to download PDAC-A ST1, I opened this link, but I could not find files including filtered_feature_bc_matrix.tsv, tissue_positions_list_spatial_object.tsv, and lowres_rot.jpg.

Would you provide a more detailed description on downloading PDAC data? Thanks.

Best,
Jia

Hello, I am currently running the SPOTlight package and attempting the spotlight decomposition portion of the. code on my reference scRNAseq data. The code I am running is below:
#Spotlight decomposition
set.seed(123)
spotlight_ls <-spotlight_deconvolution(
se_sc = E14_sc,
counts_spatial = anterior@assays$RNA@counts,
clust_vr = "subclass", # Variable in sc_seu containing the cell-type annotation
cluster_markers = cluster_markers_all, # Dataframe with the marker genes
cl_n = 100, # number of cells per cell type to use
hvg = 3000, # Number of HVG to use
ntop = NULL, # How many of the marker genes to use (by default all)
transf = "uv", # Perform unit-variance scaling per cell and spot prior to factorzation and NLS
method = "nsNMF", # Factorization method
min_cont = 0 # Remove those cells contributing to a spot below a certain threshold
)

When I run this code, I get the following error: Error in spotlight_deconvolution(se_sc = E14_sc, counts_spatial = anterior@assays$RNA@counts, :
could not find function "spotlight_deconvolution"

Here are all of the libraries I have loaded:
library(NMF)
library(SPOTlight)
library(Matrix)
library(data.table)
library(Seurat)
library(SeuratData)
library(dplyr)
library(gt)
library(igraph)
library(RColorBrewer)
library(ggplot2)
library(purrr)
library(nnls)
library(scrattch.io)
library(Spaniel)
library(igraph)
library(SeuratDisk)
library(future)

Here is my SessionInfo:
version R version 4.1.2 (2021-11-01)
os macOS Monterey 12.0.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Denver
date 2022-01-23
rstudio 2021.09.0+351 Ghost Orchid (desktop)
pandoc 2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)

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[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library

Thank you for any help!

Hello @MarcElosua ,

Thanks for sharing these files. I cannot find the coordinates of each spot in the image of PDAC data. I just saw the relative spatial positions of all spots, but I would like to map these spots to the tissue images. Thus, I need the spot's coordinates in the tissue image. Could you please help me with this? Thanks a lot!