Please read through the information below before submitting your issue to our GitHub page. The link to report an issue can be found at the bottom of the page.

GitHub Issues Guidelines

Some Useful Commands

It is helpful if you provide any relevant information about the software and Giotto object you are using. See below for some tips to get this information.

  • What version of R are you using?
R.version.string
R version 4.3.2 (2023-10-31)
  • What version of Giotto are you using?
packageVersion("Giotto")
4.0.2
  • Are you using the Giotto environment or your own python path?
# Check Giotto environment
Giotto::checkGiottoEnvironment()
giotto environment found at 
/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw
  • Show sequential processing steps/commands in the Giotto object
Giotto::showProcessingSteps(my_giotto_object)
Processing steps: 
0_normalize 

 1_subset 

 2_filter 
     name info:  tag tag 

 3_feat_stats 

 4_cell_stats 

 5_hvf 
     name info:  hvf HVFplot 

 6_pca 

 7_umap 

 8_tsne 

 9_nn_network 

 10_cluster 
     name info:  leiden_clus sNN.pca 

 11_delaunay_spatial_network 
     name info:  Delaunay_network 

 12_spatial_network 
     name info:  spatial_network 

 13_create_metafeat 
     name info:  cluster_metagene 

 14_pca 
     name info:  custom_pca 

 15_umap 
     name info:  custom_pca custom_umap 

 16_nn_network 
     name info:  custom_pca custom_NN 

 17_cluster 
     name info:  custom_leiden custom_NN
  • Show the structure of the Giotto object
str(my_giotto_object, max.level = 3)
Formal class 'giotto' [package "Giotto"] with 23 slots
  ..@ expression         :List of 1
  .. ..$ cell:List of 1
  ..@ expression_feat    : chr "rna"
  ..@ spatial_locs       :List of 1
  .. ..$ cell:List of 1
  ..@ spatial_info       : NULL
  ..@ cell_metadata      :List of 1
  .. ..$ cell:List of 1
  ..@ feat_metadata      :List of 1
  .. ..$ cell:List of 1
  ..@ feat_info          : NULL
  ..@ cell_ID            :List of 1
  .. ..$ cell: chr [1:624] "AAAGGGATGTAGCAAG-1" "AAATGGCATGTCTTGT-1" "AAATGGTCAATGTGCC-1" "AAATTAACGGGTAGCT-1" ...
  ..@ feat_ID            :List of 1
  .. ..$ rna: chr [1:634] "Gna12" "Ccnd2" "Btbd17" "Sox9" ...
  ..@ spatial_network    :List of 1
  .. ..$ cell:List of 2
  ..@ spatial_grid       : NULL
  ..@ spatial_enrichment :List of 1
  .. ..$ cell:List of 1
  ..@ dimension_reduction:List of 1
  .. ..$ cells:List of 1
  ..@ nn_network         :List of 1
  .. ..$ cell:List of 1
  ..@ images             : NULL
  ..@ largeImages        :List of 1
  .. ..$ image:Formal class 'giottoLargeImage' [package "Giotto"] with 13 slots
  ..@ parameters         :List of 18
  .. ..$ 0_normalize                : Named chr [1:14] "mini_visium" "raw" "standard" "TRUE" ...
  .. .. ..- attr(*, "names")= chr [1:14] "gobject" "expression_values" "norm_methods" "library_size_norm" ...
  .. ..$ 1_subset                   : Named chr [1:12] "gobject" "spat_unit" "feat_type" "selected_cell_ids" ...
  .. .. ..- attr(*, "names")= chr [1:12] "gobject" "spat_unit" "feat_type" "cell_ids" ...
  .. ..$ 2_filter                   : Named chr [1:13] "mini_visium" "raw" "1" "5" ...
  .. .. ..- attr(*, "names")= chr [1:13] "gobject" "expression_values" "expression_threshold" "feat_det_in_min_cells" ...
  .. ..$ 3_feat_stats               : Named chr [1:4] "mini_visium" "normalized" "0" "TRUE"
  .. .. ..- attr(*, "names")= chr [1:4] "gobject" "expression_values" "detection_threshold" "return_gobject"
  .. ..$ 4_cell_stats               : Named chr [1:4] "mini_visium" "normalized" "0" "TRUE"
  .. .. ..- attr(*, "names")= chr [1:4] "gobject" "expression_values" "detection_threshold" "return_gobject"
  .. ..$ 5_hvf                      : Named chr [1:17] "mini_visium" "normalized" "cov_groups" "FALSE" ...
  .. .. ..- attr(*, "names")= chr [1:17] "gobject" "expression_values" "method" "reverse_log_scale" ...
  .. ..$ 6_pca                      : Named chr [1:15] "mini_visium" "normalized" "cells" "hvf" ...
  .. .. ..- attr(*, "names")= chr [1:15] "gobject" "expression_values" "reduction" "feats_to_use" ...
  .. ..$ 7_umap                     : Named chr [1:17] "mini_visium" "normalized" "cells" "pca" ...
  .. .. ..- attr(*, "names")= chr [1:17] "gobject" "expression_values" "reduction" "dim_reduction_to_use" ...
  .. ..$ 8_tsne                     : Named chr [1:14] "mini_visium" "normalized" "cells" "pca" ...
  .. .. ..- attr(*, "names")= chr [1:14] "gobject" "expression_values" "reduction" "dim_reduction_to_use" ...
  .. ..$ 9_nn_network               : Named chr [1:11] "mini_visium" "sNN" "pca" "1:5" ...
  .. .. ..- attr(*, "names")= chr [1:11] "gobject" "type" "dim_reduction_to_use" "dimensions_to_use" ...
  .. ..$ 10_cluster                 : Named chr [1:11] "mini_visium" "leiden_clus" "sNN" "sNN.pca" ...
  .. .. ..- attr(*, "names")= chr [1:11] "gobject" "name" "nn_network_to_use" "network_name" ...
  .. ..$ 11_delaunay_spatial_network: Named chr [1:4] "dimensions: sdimx and sdimy" "deldir" "auto" "Delaunay_network"
  .. .. ..- attr(*, "names")= chr [1:4] "dimensions used" "method" "maximum distance threshold" "name of spatial network"
  .. ..$ 12_spatial_network         : Named chr [1:4] "10" "all" "400" "spatial_network"
  .. .. ..- attr(*, "names")= chr [1:4] "k neighbours" "dimensions used" "maximum distance threshold" "name of spatial network"
  .. ..$ 13_create_metafeat         : Named chr [1:5] "mini_visium" "normalized" "cluster_genes" "cluster_metagene" ...
  .. .. ..- attr(*, "names")= chr [1:5] "gobject" "expression_values" "feat_clusters" "name" ...
  .. ..$ 14_pca                     : Named chr [1:16] "mini_visium" "normalized" "cells" "custom_pca" ...
  .. .. ..- attr(*, "names")= chr [1:16] "gobject" "expression_values" "reduction" "name" ...
  .. ..$ 15_umap                    : Named chr [1:19] "mini_visium" "normalized" "cells" "pca" ...
  .. .. ..- attr(*, "names")= chr [1:19] "gobject" "expression_values" "reduction" "dim_reduction_to_use" ...
  .. ..$ 16_nn_network              : Named chr [1:13] "mini_visium" "sNN" "pca" "custom_pca" ...
  .. .. ..- attr(*, "names")= chr [1:13] "gobject" "type" "dim_reduction_to_use" "dim_reduction_name" ...
  .. ..$ 17_cluster                 : Named chr [1:11] "mini_visium" "custom_leiden" "sNN" "custom_NN" ...
  .. .. ..- attr(*, "names")= chr [1:11] "gobject" "name" "nn_network_to_use" "network_name" ...
  ..@ instructions       :List of 13
  .. ..$ python_path     : chr "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"
  .. ..$ show_plot       : logi TRUE
  .. ..$ return_plot     : logi FALSE
  .. ..$ save_plot       : logi FALSE
  .. ..$ save_dir        : logi NA
  .. ..$ plot_format     : chr "png"
  .. ..$ dpi             : num 300
  .. ..$ units           : chr "in"
  .. ..$ height          : num 9
  .. ..$ width           : num 9
  .. ..$ is_docker       : logi FALSE
  .. ..$ active_spat_unit: chr "cell"
  .. ..$ active_feat_type: chr "rna"
  ..@ offset_file        : NULL
  ..@ OS_platform        : chr "unix"
  ..@ join_info          : NULL
  ..@ multiomics         : NULL
  ..@ h5_file            : NULL

Warning Messages

  • Deprecation warning
my_giotto_object <- createGiottoObject(raw_exprs = "path/to/expression/data",
                                       spatial_locs = "path/to/spatial/data")
Warning message:
In createGiottoObject(raw_exprs = "/Users/username/path/to/data",  :
    raw_exprs argument is deprecated, use expression argument in the future 

Solution The code has still run and your object has been created, but in the future use the following command:

my_giotto_object <- createGiottoObject(expression = "path/to/expression/data",
                                       spatial_locs = "path/to/spatial/data")

Errors

  • Is this an error from Giotto?
Error in adjustGiottoMatrix(gobject = my_giotto_object, expression_values = c("normalized"): covariate column name(s) were not found in the cell metadata 

Solution In this case, you would need to check your cell metadata (my_giotto_object@cell_metadata) and make appropriate adjustments.

  • Is this an error from an external package?
Error in methods::as(as.matrix(x[, -1]), "Matrix") : 
no method or default for coercing "matrix" to "Matrix"

Solution Ensure that the Matrix library is loaded:

Some steps before posting an issue

  • Google (or whichever search engine you prefer) the error
  • Look up the documentation for the package the error came from

Required information to provide

  • What code/data did you use? (copy-pasted or an example is helpful)
  • What did you expect your result to be?
  • What was your result?
  • If your result was an error message, please see the category on error messages to determine whether the source was Giotto or an external package.

How to create a reproducible example

For us to be able to help you at the best of our ability, it's helpful if you can provide a reproducible example. This just means that anyone who reads your GitHub issue should be able to accurately reproduce your error.

For more information on minimal reproducible examples check out this link.

And to see what other people recommend, please check out this forum.

Example of a Good GitHub issue

  • Provide a code example
  • Please use the GitHub “insert code” function or wrap your code like so:
`x <- "hello world"

print(x)`

If applicable, provide a screenshot of the issue

I am having trouble adjusting my Giotto matix. I have inputted the following code:

my_giotto_object <- GiottoData::loadGiottoMini("visium")

my_giotto_object <- adjustGiottoMatrix(gobject = my_giotto_object, 
                                       expression_values = c('normalized'),
                                       covariate_columns = c('nr_genes',
                                                             'total_expr'))

I expected that my matrix would be appropriately adjusted, but I got the following error:

Error in adjustGiottoMatrix(gobject = my_giotto_object, expression_values = c("normalized"): covariate column name(s) were not found in the cell metadata 

For more context, I am running R version 4.3.2 and Giotto version 4.0.2. I can send you the data I used if necessary.

Example of a Bad GitHub issue

I am having trouble adjusting my Giotto matrix. My error says that the covariate column name(s) were not found in the cell meta data. What do I do?

Report An Issue https://github.com/drieslab/Giotto/issues