Error in path_to_matrix in tutorial examples

[wyq977]

Hi, when I was running some tutorials examples on Giotto site. I found out there's a typo: the location/path the path_to_matrix in Giotto sample data.

Can be checked, Giotto_1.1.1

list.files(system.file("extdata", package = 'Giotto'), recursive = T, full.names = T)

Basically, for all path_to_matrix, it should be seqfish_field_expr.txt.gz instead of seqfish_field_expr.txt.

 [1] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/datasets.txt"              
 [2] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/deg_image.png"             
 [3] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/deg_image2.png"            
 [4] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/mouse_ligand_receptors.txt"
 [5] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/seqfish_field_expr.txt.gz" 
 [6] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/seqfish_field_locs.txt"    
 [7] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/sig_matrix.txt"            
 [8] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/starmap_cell_loc.txt"      
 [9] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/starmap_expr.txt.gz"       
[10] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/visium_DG_expr.txt.gz"     
[11] "/Users/wyq977/projects/r_project/renv/library/R-4.2/aarch64-apple-darwin20/Giotto/extdata/visium_DG_locs.txt"  

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.2

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] Giotto_1.1.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3      magrittr_2.0.3    tidyselect_1.1.2  munsell_0.5.0     lattice_0.20-45   colorspace_2.0-3  R6_2.5.1          rlang_1.0.2      
 [9] fansi_1.0.3       dplyr_1.0.9       tools_4.2.0       parallel_4.2.0    grid_4.2.0        data.table_1.14.2 gtable_0.3.0      png_0.1-7        
[17] R.oo_1.24.0       utf8_1.2.2        cli_3.3.0         ellipsis_0.3.2    tibble_3.1.7      lifecycle_1.0.1   crayon_1.5.1      Matrix_1.4-1     
[25] purrr_0.3.4       ggplot2_3.3.6     vctrs_0.4.1       R.utils_2.11.0    glue_1.6.2        compiler_4.2.0    pillar_1.7.0      R.methodsS3_1.8.1
[33] generics_0.1.2    scales_1.2.0      jsonlite_1.8.0    reticulate_1.24   renv_0.15.4       pkgconfig_2.0.3 

[wyq977]

@RubD let me know if u got the time to fix it or ill close it

[drieslab]

Hi @wyq977 I've updated the website. It took us a bit longer than expected because we had to make some additional updates. I think the examples have the proper filenames now, but let me know if anything is not working as expected. Thanks

[wyq977]

No worries, I'll reopen the issue should I encounter any bugs on the website later.