Skip to content

Commit

Permalink
make it optional to change the gene name to lower case
Browse files Browse the repository at this point in the history
  • Loading branch information
Hejin Huang committed Aug 15, 2022
1 parent e881b67 commit 52620d5
Show file tree
Hide file tree
Showing 2 changed files with 2 additions and 2 deletions.
2 changes: 1 addition & 1 deletion tutorial_tangram_with_squidpy.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -587,7 +587,7 @@
"- Ensure consistent gene order in the datasets (_Tangram_ requires that the the $j$-th column in each matrix correspond to the same gene).\n",
"- If the counts for a gene are all zeros in one of the datasets, the gene is removed from the training genes.\n",
"- If a gene is not present in both datasets, the gene is removed from the training genes.\n",
"- if the gene names in single cell and spatial transcriptomics data are different due to inconsistent capitalization, we can set in the tg.pp_adatas function gene_to_lowercase = True to convert the whole name to the lower case"
"- In the pp_adatas function, the gene names are converted to lower case to get rid of the inconsistent capitalization. If this is not wanted, you can set the parameter gene_to_lowercase = False "
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion tutorial_tangram_without_squidpy.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -444,7 +444,7 @@
"- Also, the gene order needs to be the same in the datasets. This is because Tangram maps using only gene expression, so the $j$-th column in each matrix must correspond to the same gene.\n",
"- And if data entries of a gene are all zero, this gene will be removed\n",
"- This task is performed by the helper `pp_adatas`.\n",
"- In the pp_adatas function, the gene names are converted to lower case to get rid of the inconsistent capitalization. If the gene names in single cell and spatial transcriptomics data are different due to inconsistent capitalization, we can set in the tg.pp_adatas function gene_to_lowercase = True to convert the whole name to the lower case"
"- In the pp_adatas function, the gene names are converted to lower case to get rid of the inconsistent capitalization. If this is not wanted, you can set the parameter gene_to_lowercase = False "
]
},
{
Expand Down

0 comments on commit 52620d5

Please sign in to comment.