From 32e05f176f575eb9aa093048889c56a9bc5aacbc Mon Sep 17 00:00:00 2001 From: MKanetscheider <141252989+MKanetscheider@users.noreply.github.com> Date: Sat, 23 Nov 2024 10:46:38 +0100 Subject: [PATCH 1/4] Update src/scirpy/pl/_logoplots.py Co-authored-by: Gregor Sturm --- src/scirpy/pl/_logoplots.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/scirpy/pl/_logoplots.py b/src/scirpy/pl/_logoplots.py index 810ac4c30..170bad87a 100644 --- a/src/scirpy/pl/_logoplots.py +++ b/src/scirpy/pl/_logoplots.py @@ -13,6 +13,7 @@ @DataHandler.inject_param_docs() def logoplot_cdr3_motif( adata: DataHandler.TYPE, + *, chains: Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"] | Sequence[Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"]] = "VDJ_1", airr_mod="airr", airr_key="airr", From afcafa0552649ba65d7d1032e5d439ce78901364 Mon Sep 17 00:00:00 2001 From: MKanetscheider <141252989+MKanetscheider@users.noreply.github.com> Date: Sat, 23 Nov 2024 10:46:46 +0100 Subject: [PATCH 2/4] Update src/scirpy/pl/_logoplots.py Co-authored-by: Gregor Sturm --- src/scirpy/pl/_logoplots.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/scirpy/pl/_logoplots.py b/src/scirpy/pl/_logoplots.py index 170bad87a..52dca3cae 100644 --- a/src/scirpy/pl/_logoplots.py +++ b/src/scirpy/pl/_logoplots.py @@ -15,9 +15,9 @@ def logoplot_cdr3_motif( adata: DataHandler.TYPE, *, chains: Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"] | Sequence[Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"]] = "VDJ_1", - airr_mod="airr", - airr_key="airr", - chain_idx_key="chain_indices", + airr_mod: str="airr", + airr_key: str="airr", + chain_idx_key: str="chain_indices", cdr3_col: str = "junction_aa", to_type: Sequence[Literal["information", "counts", "probability", "weight"]] = "information", pseudocount: float = 0, From 2ac8e27eddeff49ff86bb477f8297d595e295064 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 23 Nov 2024 09:46:48 +0000 Subject: [PATCH 3/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/scirpy/pl/_logoplots.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/scirpy/pl/_logoplots.py b/src/scirpy/pl/_logoplots.py index 52dca3cae..33e192024 100644 --- a/src/scirpy/pl/_logoplots.py +++ b/src/scirpy/pl/_logoplots.py @@ -13,7 +13,7 @@ @DataHandler.inject_param_docs() def logoplot_cdr3_motif( adata: DataHandler.TYPE, - *, + *, chains: Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"] | Sequence[Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"]] = "VDJ_1", airr_mod: str="airr", airr_key: str="airr", From b5326b8dabed0fde9c3438165dfa9ef6da095059 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 23 Nov 2024 09:47:00 +0000 Subject: [PATCH 4/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/scirpy/pl/_logoplots.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/scirpy/pl/_logoplots.py b/src/scirpy/pl/_logoplots.py index 33e192024..0c9dfeaae 100644 --- a/src/scirpy/pl/_logoplots.py +++ b/src/scirpy/pl/_logoplots.py @@ -15,9 +15,9 @@ def logoplot_cdr3_motif( adata: DataHandler.TYPE, *, chains: Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"] | Sequence[Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"]] = "VDJ_1", - airr_mod: str="airr", - airr_key: str="airr", - chain_idx_key: str="chain_indices", + airr_mod: str = "airr", + airr_key: str = "airr", + chain_idx_key: str = "chain_indices", cdr3_col: str = "junction_aa", to_type: Sequence[Literal["information", "counts", "probability", "weight"]] = "information", pseudocount: float = 0,