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.
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.
R.version.stringR version 4.3.2 (2023-10-31)
packageVersion("Giotto")4.0.2
# Check Giotto environment
Giotto::checkGiottoEnvironment()giotto environment found at
/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw
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
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
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")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.
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:
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.
`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.
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