From 562cb1dbd0968bde54dcaa4bc0bbbb7dc4b98a14 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Mon, 26 Feb 2024 15:38:41 +0000
Subject: [PATCH 01/22] Create pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 28 +++++++++++++++++++++++
1 file changed, 28 insertions(+)
create mode 100644 docs/yaml_docs/pipeline_clustering_yml.md
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
new file mode 100644
index 00000000..6a2bf8d7
--- /dev/null
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -0,0 +1,28 @@
+
+
+# Clustering YAML
+
+In this documentation, the parameters of the `clustering` configuration yaml file are explained.
+This file is generated running `panpipes clustering config`.
+The individual steps run by the pipeline are described in [clustering worlfow](https://panpipes-pipelines.readthedocs.io/en/latest/workflows/clustering.html)
+
+When running the clustering workflow, panpipes provides a basic `pipeline.yml` file.
+To run the workflow on your own data, you need to specify the parameters described below in the `pipeline.yml` file to meet the requirements of your data.
+
+However, we do provide pre-filled versions of the `pipeline.yml` file for individual [tutorials](https://panpipes-pipelines.readthedocs.io/en/latest/tutorials/index.html).
+For more information on functionalities implemented in `panpipes` to read the configuration files, such as reading blocks of parameters and reusing blocks with `&anchors` and `*scalars`, please check [our documentation](./useful_info_on_yml.md)
+
+You can download the different clustering pipeline.yml files here:
+- Basic `pipeline.yml` file (not prefilled) that is generated when calling `panpipes clustering config`: [Download here](https://github.com/DendrouLab/panpipes/blob/main/panpipes/panpipes/pipeline_clustering/pipeline.yml)
+- `pipeline.yml` for [Clustering Tutorial](https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/3895aa0ba60017b15ee1aa6531dc8c25/pipeline.ym)
+
+## Compute resources options
+
From 8ff37a385f9929e041cc69b910df8ed8382efb46 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:57:42 +0000
Subject: [PATCH 02/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 6a2bf8d7..28fc5298 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -26,3 +26,22 @@ You can download the different clustering pipeline.yml files here:
## Compute resources options
+- resources
+Computing resources to use, specifically the number of threads used for parallel jobs.
+Specified by the following three parameters:
+ - threads_high `Integer`, Default: 2
+ Number of threads used for high intensity computing tasks.
+ For each thread, there must be enough memory to load all your input files at once and create the MuData object.
+
+ - threads_medium `Integer`, Default: 2
+ Number of threads used for medium intensity computing tasks.
+ For each thread, there must be enough memory to load your mudata and do computationally light tasks.
+
+ - threads_low `Integer`, Default: 2
+ Number of threads used for low intensity computing tasks.
+ For each thread, there must be enough memory to load text files and do plotting, requires much less memory than the other two.
+ - fewer_jobs `Boolean`, Default: True
+
+ - condaenv `String` (Path)
+ Path to conda environment that should be used to run panpipes.
+ Leave blank if running native or your cluster automatically inherits the login node environment
From 66339f19100f5c6c15c9a128ca8f4901de5db002 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 27 Feb 2024 14:07:21 +0000
Subject: [PATCH 03/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 28fc5298..569ac974 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -45,3 +45,22 @@ Specified by the following three parameters:
- condaenv `String` (Path)
Path to conda environment that should be used to run panpipes.
Leave blank if running native or your cluster automatically inherits the login node environment
+
+## Loading and merging data options
+### Data format
+
+- sample_prefix `String`, Mandatory parameter, Default: mdata
+Prefix for the sample that comes out of the filtering/ preprocessing steps of the workflow.
+
+
+- scaled_obj `String`, Mandatory parameter, Default: mdata_scaled.h5mu
+ Path to the output file from preprocessing (e.g. `../preprocess/mdata_scaled.h5mu`).
+ Ensure that the submission file must be in the right format and that the right path is provided. In this case panpipes will use the full object to calculate rank_gene_groups and for plotting those genes. If your scaled_obj contains all the genes then leave full_obj blank
+
+- full_obj `String`, Default:
+
+- modalities
+ - rna `Boolean`, Default: True
+ - prot `Boolean`, Default: True
+ - atac `Boolean`, Default: False
+ - spatial `Boolean`, Default: False
From 848b309be248ba39931533fb69a296dfaba1f126 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 27 Feb 2024 14:22:41 +0000
Subject: [PATCH 04/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 569ac974..3234542b 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -64,3 +64,11 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- prot `Boolean`, Default: True
- atac `Boolean`, Default: False
- spatial `Boolean`, Default: False
+ Run clustering on each individual modality.
+
+- moltimodal
+ - rna_clustering `Boolean`, Default: True
+ - integration_method `String`, Default: WNN
+ Options here include WNN, moda, and totalVI, and it tells us where to look for.
+
+### Parameters for finding neighbours
From d9f6b91c1c00e7f078d5d8775aac8c4699adc659 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 27 Feb 2024 15:29:50 +0000
Subject: [PATCH 05/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 81 ++++++++++++++++++++++-
1 file changed, 78 insertions(+), 3 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 3234542b..e9a4d1cd 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -46,7 +46,7 @@ Specified by the following three parameters:
Path to conda environment that should be used to run panpipes.
Leave blank if running native or your cluster automatically inherits the login node environment
-## Loading and merging data options
+## Loading data
### Data format
- sample_prefix `String`, Mandatory parameter, Default: mdata
@@ -55,7 +55,7 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- scaled_obj `String`, Mandatory parameter, Default: mdata_scaled.h5mu
Path to the output file from preprocessing (e.g. `../preprocess/mdata_scaled.h5mu`).
- Ensure that the submission file must be in the right format and that the right path is provided. In this case panpipes will use the full object to calculate rank_gene_groups and for plotting those genes. If your scaled_obj contains all the genes then leave full_obj blank
+ Ensure that the submission file must be in the right format and that the right path is provided. In this case, panpipes will use the full object to calculate rank_gene_groups and for plotting those genes. If your scaled_obj contains all the genes then leave full_obj blank
- full_obj `String`, Default:
@@ -71,4 +71,79 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- integration_method `String`, Default: WNN
Options here include WNN, moda, and totalVI, and it tells us where to look for.
-### Parameters for finding neighbours
+## Parameters for finding neighbours
+
+- neighors:
+ Sets the number of neighbors to use when calculating the graph for clustering and umap.
+ - rna:
+
+ - use_existing `Boolean`, Default: True
+ - dim_red `String`, Default: X_pca
+ Defines which representation in .obsm to use for nearest neighbors
+ - n_dim_red `Integer`, Default: 30
+ Number of components to use for clustering
+ - k `Integer`, Default: 30
+ Number of neighbours
+ - metric `String`, Default: euclidean
+ Options here include euclidean and cosine
+ - method `String`, Default: scanpy
+ Options include scanpy and hnsw (from scvelo)
+
+
+ - prot:
+
+ - use_existing `Boolean`, Default: True
+ - dim_red `String`, Default: X_pca
+ Defines which representation in .obsm to use for nearest neighbors
+ - n_dim_red `Integer`, Default: 30
+ Number of components to use for clustering
+ - k `Integer`, Default: 30
+ Number of neighbours
+ - metric `String`, Default: euclidean
+ Options here include euclidean and cosine
+ - method `String`, Default: scanpy
+ Options include scanpy and hnsw (from scvelo)
+
+
+ - atac:
+
+ - use_existing `Boolean`, Default: True
+ - dim_red `String`, Default: X_lsi
+ Defines which representation in .obsm to use for nearest neighbors
+ - n_dim_red `Integer`, Default: 1
+ Number of components to use for clustering
+ - k `Integer`, Default: 30
+ Number of neighbours
+ - metric `String`, Default: euclidean
+ Options here include euclidean and cosine
+ - method `String`, Default: scanpy
+ Options include scanpy and hnsw (from scvelo)
+
+
+
+ - spatial:
+
+ - use_existing `Boolean`, Default: False
+ - dim_red `String`, Default: X_pca
+ Defines which representation in .obsm to use for nearest neighbors
+ - n_dim_red `Integer`, Default: 30
+ Number of components to use for clustering
+ - k `Integer`, Default: 30
+ Number of neighbours
+ - metric `String`, Default: euclidean
+ Options here include euclidean and cosine
+ - method `String`, Default: scanpy
+ Options include scanpy and hnsw (from scvelo)
+
+## Parameters for umap calculation
+
+
+ - umap:
+
+ - run `Boolean`, Default: True
+ - rna:
+ - mindist `Float`, Default: 0.25 0.5
(AAAAAAAAAASSSSSSKKKKKKK)
+
+
+
+
From 42de436fa0dd1d72451ba9374d8c1e67ea41cfad Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 27 Feb 2024 15:53:34 +0000
Subject: [PATCH 06/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index e9a4d1cd..49fcc827 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -142,8 +142,18 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- run `Boolean`, Default: True
- rna:
- - mindist `Float`, Default: 0.25 0.5
(AAAAAAAAAASSSSSSKKKKKKK)
-
+ - mindist `Float`, Default: 0.25 0.5
+ Use both values as defaults.
+ - prot:
+ - mindist `Float`, Default: 0.1
+ - atac:
+ - mindist `Float`, Default: 0.5
+ - multimodal:
+ - mindist `Float`, Default: 0.5
+ - rna:
+ - mindist `Float`, Default: 0.25 0.5
+ Use both values as defaults.
+
From 0053fc28dd50e6efd2bd876e474e8cc2ab89ce93 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 27 Feb 2024 16:02:07 +0000
Subject: [PATCH 07/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 32 +++++++++++++++++++++--
1 file changed, 30 insertions(+), 2 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 49fcc827..0c46b81b 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -142,7 +142,7 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- run `Boolean`, Default: True
- rna:
- - mindist `Float`, Default: 0.25 0.5
+ - mindist `Float`, Default: 0.25, 0.5
Use both values as defaults.
- prot:
- mindist `Float`, Default: 0.1
@@ -151,9 +151,37 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- multimodal:
- mindist `Float`, Default: 0.5
- rna:
- - mindist `Float`, Default: 0.25 0.5
+ - mindist `Float`, Default: 0.25, 0.5
Use both values as defaults.
+## Parameters for clustering
+ - clusterspecs:
+ - rna:
+ - resolutions `Float`, Default: 0.2, 0.6, 1
+ Use all values as defaults.
+ - algorithm `String`, Default: leiden
+ Options include louvain or leiden.
+ - prot:
+ - resolutions `Float`, Default: 0.2, 0.6, 1
+ Use all values as defaults.
+ - algorithm `String`, Default: leiden
+ Options include louvain or leiden.
+ - atac:
+ - resolutions `Float`, Default: 0.2, 0.6, 1
+ Use all values as defaults.
+ - algorithm `String`, Default: leiden
+ Options include louvain or leiden.
+ - multimmodal:
+ - resolutions `Float`, Default: 0.5, 0.7
+ Use all values as defaults.
+ - algorithm `String`, Default: leiden
+ Options include louvain or leiden.
+
+ - spatial:
+ - resolutions `Float`, Default: 0.2, 0.6, 1
+ Use all values as defaults.
+ - algorithm `String`, Default: leiden
+ Options include louvain or leiden.
From 9100c9b7685c8b6cf4099874722f5ddd4d731d41 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 27 Feb 2024 16:39:58 +0000
Subject: [PATCH 08/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 81 +++++++++++++++++++++++
1 file changed, 81 insertions(+)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 0c46b81b..318f039c 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -185,3 +185,84 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- algorithm `String`, Default: leiden
Options include louvain or leiden.
+## Parameters for finding marker genes
+If pseudo_suerat is set to false then we run [scanpy](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.rank_genes_groups.html).
+When pseudo_seurat is set to true then a python implementation of Suerat runs (Seurat::FindMarkers written by CRG)
+
+ - markerspecs:
+ - rna:
+ - run `Boolean`, Default: True
+ - layer `String`, Default: logged_counts
+ - method `String`, Default: t-test_overestim_var
+ Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
+ - mincels `Integer`, Default: t-10
+ If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ - pseudo_seurat `Boolean`, Default: False
+ - minpct `Float`, Default: 0.1
+ This parameter only matters if pseudo_seurat is set to True
+ - threshuse `Float`, Default: 0.25
+ This parameter only matters if pseudo_seurat is set to True
+
+ - prot:
+ - run `Boolean`, Default: True
+ - layer `String`, Default: clr
+ Options include clr and dsb.
+ - mincels `Integer`, Default: t-10
+ If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ - method `String`, Default: wilcoxon
+ - pseudo_seurat `Boolean`, Default: False
+ - minpct `Float`, Default: 0.1
+ This parameter only matters if pseudo_seurat is set to True
+ - threshuse `Float`, Default: 0.25
+ This parameter only matters if pseudo_seurat is set to True
+
+ - atac:
+ - run `Boolean`, Default: False
+ - layer `String`, Default: logged_counts
+ Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
+ - mincels `Integer`, Default: t-10
+ If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ - method `String`, Default: wilcoxon
+ Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
+ - pseudo_seurat `Boolean`, Default: False
+ - minpct `Float`, Default: 0.1
+ This parameter only matters if pseudo_seurat is set to True
+ - threshuse `Float`, Default: 0.25
+ This parameter only matters if pseudo_seurat is set to True
+
+
+ - multimodal:
+ - mincels `Integer`, Default: t-10
+ If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ - method `String`, Default: wilcoxon
+ Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
+ - pseudo_seurat `Boolean`, Default: False
+ - minpct `Float`, Default: 0.1
+ This parameter only matters if pseudo_seurat is set to True
+ - threshuse `Float`, Default: 0.25
+ This parameter only matters if pseudo_seurat is set to True
+
+
+ - spatial:
+ - run `Boolean`, Default: True
+ - layer `String`, Default: norm_pearson_resid
+ Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
+ - method `String`, Default: t-test_overestim_var
+ Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
+ - mincels `Integer`, Default: t-10
+ If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ - pseudo_seurat `Boolean`, Default: False
+ - minpct `Float`, Default: 0.1
+ This parameter only matters if pseudo_seurat is set to True
+ - threshuse `Float`, Default: 0.25
+ This parameter only matters if pseudo_seurat is set to True
+
+## Plot specifications
+Used to define which metadata columns are used in the visualisations
+ - plotspecs:
+ - layers:
+ - rna `String`, Default: logged_counts
+ - prot `String`, Default: clr
+ - atac `String`, Default: signac_norm
+ - spacial `?`, Default: ?
(CHEEECKKKKK)
+ - top_n_markers `Integer`, Default: 10
From 6ad1bf022e267231db1b9cb8346ebdddc26185db Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Wed, 28 Feb 2024 10:41:03 +0000
Subject: [PATCH 09/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 318f039c..79252630 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -8,7 +8,7 @@
}
-# Clustering YAML
+# Clustering YAML
In this documentation, the parameters of the `clustering` configuration yaml file are explained.
This file is generated running `panpipes clustering config`.
@@ -264,5 +264,5 @@ Used to define which metadata columns are used in the visualisations
- rna `String`, Default: logged_counts
- prot `String`, Default: clr
- atac `String`, Default: signac_norm
- - spacial `?`, Default: ?
(CHEEECKKKKK)
+ - spacial `?`, Default: ?
- top_n_markers `Integer`, Default: 10
From 46ce807678cff246962f908d2f5c2cf5dd0f0653 Mon Sep 17 00:00:00 2001
From: bio-la
Date: Wed, 28 Feb 2024 13:22:33 +0100
Subject: [PATCH 10/22] added to index to review
---
docs/yaml_docs/index.rst | 1 +
1 file changed, 1 insertion(+)
diff --git a/docs/yaml_docs/index.rst b/docs/yaml_docs/index.rst
index ad028376..3fd86bc8 100644
--- a/docs/yaml_docs/index.rst
+++ b/docs/yaml_docs/index.rst
@@ -7,6 +7,7 @@ Workflows configuration files
useful_info_on_yml
pipeline_ingestion_yml
pipeline_integration_yml
+ pipeline_clustering_yml
spatial_qc
spatial_preprocess
spatial_deconvolution
\ No newline at end of file
From 94659f869209b216506e4ef1faa926b467a92fc6 Mon Sep 17 00:00:00 2001
From: bio-la
Date: Wed, 28 Feb 2024 14:17:39 +0100
Subject: [PATCH 11/22] fixes
---
docs/yaml_docs/pipeline_clustering_yml.md | 37 +++++++++++++----------
1 file changed, 21 insertions(+), 16 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 79252630..9bf3a656 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -18,11 +18,12 @@ When running the clustering workflow, panpipes provides a basic `pipeline.yml` f
To run the workflow on your own data, you need to specify the parameters described below in the `pipeline.yml` file to meet the requirements of your data.
However, we do provide pre-filled versions of the `pipeline.yml` file for individual [tutorials](https://panpipes-pipelines.readthedocs.io/en/latest/tutorials/index.html).
+
For more information on functionalities implemented in `panpipes` to read the configuration files, such as reading blocks of parameters and reusing blocks with `&anchors` and `*scalars`, please check [our documentation](./useful_info_on_yml.md)
You can download the different clustering pipeline.yml files here:
- Basic `pipeline.yml` file (not prefilled) that is generated when calling `panpipes clustering config`: [Download here](https://github.com/DendrouLab/panpipes/blob/main/panpipes/panpipes/pipeline_clustering/pipeline.yml)
-- `pipeline.yml` for [Clustering Tutorial](https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/3895aa0ba60017b15ee1aa6531dc8c25/pipeline.ym)
+- `pipeline.yml` for [Clustering Tutorial](https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/3895aa0ba60017b15ee1aa6531dc8c25/pipeline.yml)
## Compute resources options
@@ -55,10 +56,11 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- scaled_obj `String`, Mandatory parameter, Default: mdata_scaled.h5mu
Path to the output file from preprocessing (e.g. `../preprocess/mdata_scaled.h5mu`).
- Ensure that the submission file must be in the right format and that the right path is provided. In this case, panpipes will use the full object to calculate rank_gene_groups and for plotting those genes. If your scaled_obj contains all the genes then leave full_obj blank
+ Ensure that the path to the file is correct.
- full_obj `String`, Default:
-
+ Speficy the full object if your scaled_obj contains only HVG. If your scaled_obj contains all the genes then leave full_obj blank.
+ panpipes will use the full object to do marker genes analysis (rank_gene_groups) and for plotting those genes.
- modalities
- rna `Boolean`, Default: True
- prot `Boolean`, Default: True
@@ -142,46 +144,49 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- run `Boolean`, Default: True
- rna:
- - mindist `Float`, Default: 0.25, 0.5
- Use both values as defaults.
+ - mindist `Float`, Default: 0.5
+ Can specify an array: 0.25,0.5
- prot:
- - mindist `Float`, Default: 0.1
+ - mindist `Float`, Default: 0.5
+ Can specify an array: 0.25,0.5,0.8
- atac:
- mindist `Float`, Default: 0.5
+ Can specify an array: 0.25,0.5,0.8
- multimodal:
- mindist `Float`, Default: 0.5
+ Can specify an array: 0.25,0.5,0.8
- rna:
- - mindist `Float`, Default: 0.25, 0.5
- Use both values as defaults.
+ - mindist `Float`, Default: 0.5
+ Can specify an array: 0.25,0.5,0.8
## Parameters for clustering
- clusterspecs:
- rna:
- resolutions `Float`, Default: 0.2, 0.6, 1
- Use all values as defaults.
+ Can specify an array: 0.2,0.6,1
- algorithm `String`, Default: leiden
Options include louvain or leiden.
- prot:
- resolutions `Float`, Default: 0.2, 0.6, 1
- Use all values as defaults.
+ Can specify an array: 0.2,0.6,1
- algorithm `String`, Default: leiden
Options include louvain or leiden.
- atac:
- resolutions `Float`, Default: 0.2, 0.6, 1
- Use all values as defaults.
+ Can specify an array to compute in parallel: 0.2,0.6,1
- algorithm `String`, Default: leiden
Options include louvain or leiden.
- multimmodal:
- resolutions `Float`, Default: 0.5, 0.7
- Use all values as defaults.
+ Can specify an array to compute in parallel: 0.2,0.6,1
- algorithm `String`, Default: leiden
Options include louvain or leiden.
- spatial:
- resolutions `Float`, Default: 0.2, 0.6, 1
- Use all values as defaults.
+ Can specify an array to compute in parallel: 0.2,0.6,1
- algorithm `String`, Default: leiden
Options include louvain or leiden.
@@ -206,15 +211,15 @@ When pseudo_seurat is set to true then a python implementation of Suerat runs (S
- prot:
- run `Boolean`, Default: True
- layer `String`, Default: clr
- Options include clr and dsb.
+ Can specify an array to compute in parallel: clr, dsb
- mincels `Integer`, Default: t-10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- method `String`, Default: wilcoxon
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- threshuse `Float`, Default: 0.25
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- atac:
- run `Boolean`, Default: False
From 07df95220dc71b2ffe4750dd9825251c620c49a9 Mon Sep 17 00:00:00 2001
From: bio-la
Date: Wed, 28 Feb 2024 14:18:45 +0100
Subject: [PATCH 12/22] typo
---
docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 9bf3a656..d388d0c5 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -269,5 +269,5 @@ Used to define which metadata columns are used in the visualisations
- rna `String`, Default: logged_counts
- prot `String`, Default: clr
- atac `String`, Default: signac_norm
- - spacial `?`, Default: ?
+ - spatial `?`, Default: ?
- top_n_markers `Integer`, Default: 10
From 2ded3937602ec33bacf1309c59b3e2e30ab19bf4 Mon Sep 17 00:00:00 2001
From: bio-la
Date: Wed, 28 Feb 2024 14:25:52 +0100
Subject: [PATCH 13/22] fixes
---
docs/yaml_docs/pipeline_clustering_yml.md | 18 +++++++++++-------
1 file changed, 11 insertions(+), 7 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index d388d0c5..00d6df47 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -191,13 +191,16 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
Options include louvain or leiden.
## Parameters for finding marker genes
-If pseudo_suerat is set to false then we run [scanpy](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.rank_genes_groups.html).
-When pseudo_seurat is set to true then a python implementation of Suerat runs (Seurat::FindMarkers written by CRG)
+
+In this part of the analysis we define parameters to run marker analysis.
+By default, pseudo_seurat is set to False, and we run [scanpy.tl.rank_genes_groups](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.rank_genes_groups.html).
+When pseudo_seurat is set to True then a [python implementation](https://github.com/DendrouLab/panpipes/blob/main/panpipes/python_scripts/run_find_markers_multi.py) of `Seurat:::FindMarkers` is run
- markerspecs:
- rna:
- run `Boolean`, Default: True
- layer `String`, Default: logged_counts
+ Which layer stores counts for differential expression test.
- method `String`, Default: t-test_overestim_var
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- mincels `Integer`, Default: t-10
@@ -211,7 +214,7 @@ When pseudo_seurat is set to true then a python implementation of Suerat runs (S
- prot:
- run `Boolean`, Default: True
- layer `String`, Default: clr
- Can specify an array to compute in parallel: clr, dsb
+ Which layer stores counts for differential expression test.
- mincels `Integer`, Default: t-10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- method `String`, Default: wilcoxon
@@ -224,6 +227,7 @@ When pseudo_seurat is set to true then a python implementation of Suerat runs (S
- atac:
- run `Boolean`, Default: False
- layer `String`, Default: logged_counts
+ Which layer stores counts for differential expression test.
Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
- mincels `Integer`, Default: t-10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
@@ -231,9 +235,9 @@ When pseudo_seurat is set to true then a python implementation of Suerat runs (S
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- threshuse `Float`, Default: 0.25
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- multimodal:
@@ -243,9 +247,9 @@ When pseudo_seurat is set to true then a python implementation of Suerat runs (S
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- threshuse `Float`, Default: 0.25
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- spatial:
From 268cb755b58b4e09ee7769858740459416a9fc46 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Wed, 28 Feb 2024 16:26:21 +0000
Subject: [PATCH 14/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 00d6df47..9b56938f 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -207,10 +207,9 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- threshuse `Float`, Default: 0.25
- This parameter only matters if pseudo_seurat is set to True
-
+ TThis parameter is mandatory if pseudo_seurat is set to True
- prot:
- run `Boolean`, Default: True
- layer `String`, Default: clr
@@ -258,14 +257,13 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
- method `String`, Default: t-test_overestim_var
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- - mincels `Integer`, Default: t-10
+ - mincels `Integer`, Default: 10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
- This parameter only matters if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- threshuse `Float`, Default: 0.25
- This parameter only matters if pseudo_seurat is set to True
-
+ This parameter is mandatory if pseudo_seurat is set to True
## Plot specifications
Used to define which metadata columns are used in the visualisations
- plotspecs:
From 8965d4b8af8516270f909e2a4a82c54a5c35cb82 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:22:32 +0000
Subject: [PATCH 15/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 9b56938f..79d6d879 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -203,7 +203,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
Which layer stores counts for differential expression test.
- method `String`, Default: t-test_overestim_var
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- - mincels `Integer`, Default: t-10
+ - mincels `Integer`, Default: 10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
From 48fbcd293f20bfb1c39d5f86ccc04f8d173fd526 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:35:19 +0000
Subject: [PATCH 16/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 79d6d879..ac0820ed 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -5,7 +5,7 @@
padding: 4px;
display: inline-block;
font-weight: bold;
- }
+ }
# Clustering YAML
From 27d0bfa292031dbd0fe7a90c374ad4857f9856c6 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 5 Mar 2024 11:31:51 +0000
Subject: [PATCH 17/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index ac0820ed..76fd61a5 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -214,7 +214,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- run `Boolean`, Default: True
- layer `String`, Default: clr
Which layer stores counts for differential expression test.
- - mincels `Integer`, Default: t-10
+ - mincels `Integer`, Default: 10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- method `String`, Default: wilcoxon
- pseudo_seurat `Boolean`, Default: False
From 1cd393cdd6bce10eab1ef12715feac00aa98c048 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia
Date: Tue, 5 Mar 2024 11:42:38 +0000
Subject: [PATCH 18/22] changes to clustering yaml
---
docs/yaml_docs/pipeline_clustering_yml.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 76fd61a5..b34981fb 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -228,7 +228,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- layer `String`, Default: logged_counts
Which layer stores counts for differential expression test.
Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
- - mincels `Integer`, Default: t-10
+ - mincels `Integer`, Default: 10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- method `String`, Default: wilcoxon
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
@@ -240,7 +240,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- multimodal:
- - mincels `Integer`, Default: t-10
+ - mincels `Integer`, Default:10
If the number of clusters contains less than the number of cells maker analysis is not necessary.
- method `String`, Default: wilcoxon
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
From 3336992c5782c1fbd60a5e62cc9f807693b5aec9 Mon Sep 17 00:00:00 2001
From: giuliaelgarcia
Date: Tue, 12 Mar 2024 14:09:22 +0000
Subject: [PATCH 19/22] clustering_yml changes
---
docs/yaml_docs/pipeline_clustering_yml.md | 26 +++++++++++------------
1 file changed, 13 insertions(+), 13 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index b34981fb..91d4d9e9 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -12,7 +12,7 @@
In this documentation, the parameters of the `clustering` configuration yaml file are explained.
This file is generated running `panpipes clustering config`.
-The individual steps run by the pipeline are described in [clustering worlfow](https://panpipes-pipelines.readthedocs.io/en/latest/workflows/clustering.html)
+The individual steps run by the pipeline are described in [clustering workflow](https://panpipes-pipelines.readthedocs.io/en/latest/workflows/clustering.html)
When running the clustering workflow, panpipes provides a basic `pipeline.yml` file.
To run the workflow on your own data, you need to specify the parameters described below in the `pipeline.yml` file to meet the requirements of your data.
@@ -55,11 +55,11 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- scaled_obj `String`, Mandatory parameter, Default: mdata_scaled.h5mu
- Path to the output file from preprocessing (e.g. `../preprocess/mdata_scaled.h5mu`).
+ Path to the output file from preprocessing (e.g. `../preprocessed/mdata_scaled.h5mu`).
Ensure that the path to the file is correct.
- full_obj `String`, Default:
- Speficy the full object if your scaled_obj contains only HVG. If your scaled_obj contains all the genes then leave full_obj blank.
+ Specify the full object if your scaled_obj contains only HVG. If your scaled_obj contains all the genes then leave full_obj blank.
panpipes will use the full object to do marker genes analysis (rank_gene_groups) and for plotting those genes.
- modalities
- rna `Boolean`, Default: True
@@ -68,14 +68,14 @@ Prefix for the sample that comes out of the filtering/ preprocessing steps of th
- spatial `Boolean`, Default: False
Run clustering on each individual modality.
-- moltimodal
+- multimodal
- rna_clustering `Boolean`, Default: True
- integration_method `String`, Default: WNN
- Options here include WNN, moda, and totalVI, and it tells us where to look for.
+ Options here include WNN, mofa, and totalVI, and it tells us where to look for.
## Parameters for finding neighbours
-- neighors:
+- neighbors:
Sets the number of neighbors to use when calculating the graph for clustering and umap.
- rna:
@@ -204,18 +204,18 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- method `String`, Default: t-test_overestim_var
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- mincels `Integer`, Default: 10
- If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
This parameter is mandatory if pseudo_seurat is set to True
- threshuse `Float`, Default: 0.25
- TThis parameter is mandatory if pseudo_seurat is set to True
+ This parameter is mandatory if pseudo_seurat is set to True
- prot:
- run `Boolean`, Default: True
- layer `String`, Default: clr
Which layer stores counts for differential expression test.
- mincels `Integer`, Default: 10
- If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
- method `String`, Default: wilcoxon
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
@@ -229,7 +229,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
Which layer stores counts for differential expression test.
Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
- mincels `Integer`, Default: 10
- If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
- method `String`, Default: wilcoxon
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- pseudo_seurat `Boolean`, Default: False
@@ -241,7 +241,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- multimodal:
- mincels `Integer`, Default:10
- If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ If the cluster contains less than this number of cells, the marker analysis won't be run.
- method `String`, Default: wilcoxon
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- pseudo_seurat `Boolean`, Default: False
@@ -258,14 +258,14 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- method `String`, Default: t-test_overestim_var
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- mincels `Integer`, Default: 10
- If the number of clusters contains less than the number of cells maker analysis is not necessary.
+ Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
This parameter is mandatory if pseudo_seurat is set to True
- threshuse `Float`, Default: 0.25
This parameter is mandatory if pseudo_seurat is set to True
## Plot specifications
-Used to define which metadata columns are used in the visualisations
+Used to define which metadata columns are used in the visualizations
- plotspecs:
- layers:
- rna `String`, Default: logged_counts
From 2fe7016e20a0c8954e0b355155350b80e69433ba Mon Sep 17 00:00:00 2001
From: giuliaelgarcia
Date: Mon, 18 Mar 2024 15:06:19 +0000
Subject: [PATCH 20/22] changes to clustering yaml
---
docs/yaml_docs/pipeline_clustering_yml.md | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 91d4d9e9..55977e4c 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -271,5 +271,6 @@ Used to define which metadata columns are used in the visualizations
- rna `String`, Default: logged_counts
- prot `String`, Default: clr
- atac `String`, Default: signac_norm
- - spatial `?`, Default: ?
+ - spatial `String`, Default: None
+ Options include lognorm and norm_pearson_resid depending what was selected on preprocessing.
- top_n_markers `Integer`, Default: 10
From 7e1ddf33de1192c402636cb764e7a9d4151860a2 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 16 Apr 2024 15:29:56 +0100
Subject: [PATCH 21/22] Update pipeline_clustering_yml.md
---
docs/yaml_docs/pipeline_clustering_yml.md | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 55977e4c..bc5a22dd 100644
--- a/docs/yaml_docs/pipeline_clustering_yml.md
+++ b/docs/yaml_docs/pipeline_clustering_yml.md
@@ -203,8 +203,8 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
Which layer stores counts for differential expression test.
- method `String`, Default: t-test_overestim_var
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- - mincels `Integer`, Default: 10
- Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
+ - mincells `Integer`, Default: 10
+ Marker analysis is run for clusters >= mincells. If a cluster ncells < mincells , then the cluster is excluded from marker analysis
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
This parameter is mandatory if pseudo_seurat is set to True
@@ -214,8 +214,8 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- run `Boolean`, Default: True
- layer `String`, Default: clr
Which layer stores counts for differential expression test.
- - mincels `Integer`, Default: 10
- Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
+ - mincells `Integer`, Default: 10
+ Marker analysis is run for clusters >= mincells. If a cluster ncells < mincells , then the cluster is excluded from marker analysis
- method `String`, Default: wilcoxon
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
@@ -228,8 +228,8 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- layer `String`, Default: logged_counts
Which layer stores counts for differential expression test.
Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
- - mincels `Integer`, Default: 10
- Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
+ - mincells `Integer`, Default: 10
+ Marker analysis is run for clusters >= mincells. If a cluster ncells < mincells , then the cluster is excluded from marker analysis
- method `String`, Default: wilcoxon
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- pseudo_seurat `Boolean`, Default: False
@@ -240,7 +240,7 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
- multimodal:
- - mincels `Integer`, Default:10
+ - mincells `Integer`, Default:10
If the cluster contains less than this number of cells, the marker analysis won't be run.
- method `String`, Default: wilcoxon
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
@@ -257,8 +257,8 @@ When pseudo_seurat is set to True then a [python implementation](https://github.
Options include logged_counts, signac_norm , and logTF_norm,logIDF_norm
- method `String`, Default: t-test_overestim_var
Options include: ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’
- - mincels `Integer`, Default: 10
- Minimal number of cells in a cluster. If the cluster contains less than this number of cells, the marker analysis won't be run.
+ - mincells `Integer`, Default: 10
+ Marker analysis is run for clusters >= mincells. If a cluster ncells < mincells , then the cluster is excluded from marker analysis
- pseudo_seurat `Boolean`, Default: False
- minpct `Float`, Default: 0.1
This parameter is mandatory if pseudo_seurat is set to True
From 0935a7e307dc58eb1efaec4f37a349a7eb98abc5 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 16 Apr 2024 15:44:43 +0100
Subject: [PATCH 22/22] Update gene_list_format.md
---
docs/usage/gene_list_format.md | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/docs/usage/gene_list_format.md b/docs/usage/gene_list_format.md
index e1df3016..790734bf 100644
--- a/docs/usage/gene_list_format.md
+++ b/docs/usage/gene_list_format.md
@@ -151,6 +151,33 @@ minimal:
Generally in the visualization pipeline all gene groups in the input are plotted. In heatmaps and dotplots, one dotplot per group is plotted. For UMAPs, one plot per gene is
plotted, and a new file is saved per group.
+
+## Plot Makers in the Visualization workflow
+
+The custom maker csv file for full and minimal must contain three columns and follow the following structure:
+ | mod | feature | group |
+ |------|----------|--------------|
+ | prot | prot_CD8 | Tcellmarkers |
+ | rna | CD8A | Tcellmarkers |
+
+The full list will be plotted in dot plots and matrix plots, with one plot per group.
+
+The shorter list will be plotted on umaps as well as other plot types, with one plot per group.
+
+ | feature_1 | feature_2 | colour |
+ |-----------|-----------|----------------|
+ | CD8A | prot_CD8 | |
+ | CD4 | CD8A | doublet_scores |
+
+
+
+## Plot metadata variables
+The scatter_features.csv file should have the following format:
+
+ | feature_1 | feature_2 | colour |
+ |-----------|-----------|----------------|
+ |rna:total_counts | prot:total_counts | doublet_scores
+
## Final notes
Be deliberate and informative with the choice of group names for any gene set use, since the `.obs` column generated as output will be named based on the group of the gene list input file.