Error in open.connection(con, "rb") : cannot open the connection about scwat-st

[lfranzen]

Hi! Not sure I recognise the error entirely, however it looks a bit like the file paths might be the issue? Could you double check to make sure the paths in your infoTable is pointing to your data files correctly?

[dm8000]

Thank you for the reply @lfranzen

the infotable is as original. I imagined it could be a path problem as I did not edit anything, but I assumed it was working fine as the Sample meta data block loaded the table without problems

```{r create_infotable}
sample_select_ids <- metadata_selected[, "novaseq_id"]
data_proc <- "trimmed"
sample_dirs_all <- c()
sample_names_all <- c()
for (s in sample_select_ids){
  message("Fetching data path for sample ", s)
  sample_dirs <- grep(pattern = s, x = list.dirs(path = file.path(DIR_DATA), recursive = F, full.names = T), value = T)
  sample_dirs <- grep(pattern = data_proc, x = sample_dirs, value = T)
  sample_dirs_all <- c(sample_dirs_all, sample_dirs)
  
  sample_names <- grep(pattern = s, x = list.dirs(path = file.path(DIR_DATA), recursive = F, full.names = F), value = T)
  sample_names <- grep(pattern = data_proc, x = sample_names, value = T)
  sample_names_all <- c(sample_names_all, sample_names)
}

data_dirs <- paste0(sample_dirs_all, "/filtered_feature_bc_matrix.h5")
spot_dirs <- paste0(sample_dirs_all, "/spatial/tissue_positions_list.csv")
img_dirs <- paste0(sample_dirs_all, "/spatial/tissue_hires_image.png")
img_scale_dirs <- paste0(sample_dirs_all, "/spatial/scalefactors_json.json")

infoTable <- data.frame(samples = data_dirs,
                        spotfiles = spot_dirs,
                        imgs = img_dirs,
                        json = img_scale_dirs,
                        metadata_selected, 
                        stringsAsFactors = F)

I downloaded the data and put it in the data folder, but maybe I did not structured it correctly?
Here is what the data folder looks like

~/Documents/visiumadipocyte/scwat-st/data/visium$ ls
S41_trimmed  S46_trimmed  S51_trimmed  se-object.visium_baseline.rds.zip
S42_trimmed  S47_trimmed  S52_trimmed  se-object.visium_insulin.rds.zip
S43_trimmed  S48_trimmed  S53_trimmed  stereoscope_210322.zip
S44_trimmed  S49_trimmed  S54_trimmed  visium_sample_metadata.tsv
S45_trimmed  S50_trimmed  S55_trimmed

Neatly organized code btw

[lfranzen]

Thank you for the reply @lfranzen

the infotable is as original. I imagined it could be a path problem as I did not edit anything, but I assumed it was working fine as the Sample meta data block loaded the table without problems

```{r create_infotable}
sample_select_ids <- metadata_selected[, "novaseq_id"]
data_proc <- "trimmed"
sample_dirs_all <- c()
sample_names_all <- c()
for (s in sample_select_ids){
  message("Fetching data path for sample ", s)
  sample_dirs <- grep(pattern = s, x = list.dirs(path = file.path(DIR_DATA), recursive = F, full.names = T), value = T)
  sample_dirs <- grep(pattern = data_proc, x = sample_dirs, value = T)
  sample_dirs_all <- c(sample_dirs_all, sample_dirs)
  
  sample_names <- grep(pattern = s, x = list.dirs(path = file.path(DIR_DATA), recursive = F, full.names = F), value = T)
  sample_names <- grep(pattern = data_proc, x = sample_names, value = T)
  sample_names_all <- c(sample_names_all, sample_names)
}

data_dirs <- paste0(sample_dirs_all, "/filtered_feature_bc_matrix.h5")
spot_dirs <- paste0(sample_dirs_all, "/spatial/tissue_positions_list.csv")
img_dirs <- paste0(sample_dirs_all, "/spatial/tissue_hires_image.png")
img_scale_dirs <- paste0(sample_dirs_all, "/spatial/scalefactors_json.json")

infoTable <- data.frame(samples = data_dirs,
                        spotfiles = spot_dirs,
                        imgs = img_dirs,
                        json = img_scale_dirs,
                        metadata_selected, 
                        stringsAsFactors = F)

I downloaded the data and put it in the data folder, but maybe I did not structured it correctly? Here is what the data folder looks like

~/Documents/visiumadipocyte/scwat-st/data/visium$ ls
S41_trimmed  S46_trimmed  S51_trimmed  se-object.visium_baseline.rds.zip
S42_trimmed  S47_trimmed  S52_trimmed  se-object.visium_insulin.rds.zip
S43_trimmed  S48_trimmed  S53_trimmed  stereoscope_210322.zip
S44_trimmed  S49_trimmed  S54_trimmed  visium_sample_metadata.tsv
S45_trimmed  S50_trimmed  S55_trimmed

Neatly organized code btw

I see, that code should hopefully work, or at least I thought I made it so that it should work! However could you print out one example row from the infoTable and make sure the entire path are pointing to the correct locations? Especially the scalefactors_json.json files since it seems that's what the initial error was complaining about

[dm8000]

Hello @lfranzen

It seems it could have been a problem with my environment, as the code seems to run smoothly after I restarted. I ran into another problem though, which I will open another issue.

Thank you for the help!