From 2164130307334602f311c0bf9716eece5c297d10 Mon Sep 17 00:00:00 2001 From: Nikolay Akhmetov Date: Thu, 10 Aug 2023 16:57:49 -0400 Subject: [PATCH] deprecate old `obs_labels_path`, fix some markdown --- vitessce/wrappers.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/vitessce/wrappers.py b/vitessce/wrappers.py index 308b416b..a94a3e0e 100644 --- a/vitessce/wrappers.py +++ b/vitessce/wrappers.py @@ -516,15 +516,15 @@ def __init__(self, adata_path=None, adata_url=None, obs_feature_matrix_path=None :param str feature_filter_path: A string like `var/highly_variable` used in conjunction with `obs_feature_matrix_path` if obs_feature_matrix_path points to a subset of `X` of the full `var` list. :param str initial_feature_filter_path: A string like `var/highly_variable` used in conjunction with `obs_feature_matrix_path` if obs_feature_matrix_path points to a subset of `X` of the full `var` list. :param list[str] obs_set_paths: Column names like `['obs/louvain', 'obs/cellType']` for showing cell sets - :param list[str] obs_set_names: Names to display in place of those in `obs_set_paths`, like `['Louvain', 'Cell Type'] + :param list[str] obs_set_names: Names to display in place of those in `obs_set_paths`, like `['Louvain', 'Cell Type']` :param str obs_locations_path: Column name in `obsm` that contains centroid coordinates for displaying centroids in the spatial viewer :param str obs_segmentations_path: Column name in `obsm` that contains polygonal coordinates for displaying outlines in the spatial viewer :param list[str] obs_embedding_paths: Column names like `['obsm/X_umap', 'obsm/X_pca']` for showing scatterplots - :param list[str] obs_embedding_names: Overriding names like `['UMAP', 'PCA'] for displaying above scatterplots - :param list[str] obs_embedding_dims: Dimensions along which to get data for the scatterplot, like [[0, 1], [4, 5]] where [0, 1] is just the normal x and y but [4, 5] could be comparing the third and fourth principal components, for example. - :param dict request_init: options to be passed along with every fetch request from the browser, like { "header": { "Authorization": "Bearer dsfjalsdfa1431" } } + :param list[str] obs_embedding_names: Overriding names like `['UMAP', 'PCA']` for displaying above scatterplots + :param list[str] obs_embedding_dims: Dimensions along which to get data for the scatterplot, like `[[0, 1], [4, 5]]` where `[0, 1]` is just the normal x and y but `[4, 5]` could be comparing the third and fourth principal components, for example. + :param dict request_init: options to be passed along with every fetch request from the browser, like `{ "header": { "Authorization": "Bearer dsfjalsdfa1431" } }` :param str feature_labels_path: The name of a column containing feature labels (e.g., alternate gene symbols), instead of the default index in `var` of the AnnData store. - :param str obs_labels_path: The name of a column containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store. + :param str obs_labels_path: (DEPRECATED) The name of a column containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store. Use `obs_labels_paths` and `obs_labels_names` instead. This arg will be removed in a future release. :param list[str] obs_labels_paths: The names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store. :param list[str] obs_labels_names: The optional display names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store. :param bool convert_to_dense: Whether or not to convert `X` to dense the zarr store (dense is faster but takes more disk space).