biopipen 0.34.9__tar.gz → 0.34.11__tar.gz

{biopipen-0.34.9 → biopipen-0.34.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biopipen
-Version: 0.34.9
+Version: 0.34.11
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.34.11/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.34.11"

{biopipen-0.34.9 → biopipen-0.34.11}/biopipen/ns/scrna.py

@@ -118,6 +118,10 @@ class SeuratPreparing(Proc):
             It doesn't work when data is loaded from loom files.
         cell_qc: Filter expression to filter cells, using
             `tidyrseurat::filter()`.
+            It can also be a dictionary of expressions, where the names of the list are
+            sample names.
+            You can have a default expression in the list with the name "DEFAULT" for
+            the samples that are not listed.
             Available QC keys include `nFeature_RNA`, `nCount_RNA`,
             `percent.mt`, `percent.ribo`, `percent.hb`, and `percent.plat`.
 
@@ -782,7 +786,7 @@ class ModuleScoreCalculator(Proc):
             will perform diffusion map as a reduction and add the first 2
             components as `DC_1` and `DC_2` to the metadata. `diffmap` is a shortcut
             for `diffusion_map`. Other key-value pairs will pass to
-            [`destiny::DiffusionMap()`](https://www.rdocumentation.org/packages/destiny/versions/2.0.4/topics/DiffusionMap%20class).
+            [`destiny::DiffusionMap()`](https://www.rdocumentation.org/packages/destiny/versions/2.0.4/topics/DiffusionMap class).
             You can later plot the diffusion map by using
             `reduction = "DC"` in `env.dimplots` in `SeuratClusterStats`.
             This requires [`SingleCellExperiment`](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
@@ -1085,7 +1089,7 @@ class MarkersFinder(Proc):
             - <more>: See <https://satijalab.org/seurat/reference/findmarkers>
         allmarker_plots_defaults (ns): Default options for the plots for all markers when `ident-1` is not specified.
             - plot_type: The type of the plot.
-                See <https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html>.
+                See <https://pwwang.github.io/biopipen.utils.R/reference/VizDEGs.html>.
                 Available types are `violin`, `box`, `bar`, `ridge`, `dim`, `heatmap` and `dot`.
             - more_formats (type=list): The extra formats to save the plot in.
             - save_code (flag): Whether to save the code to generate the plot.
@@ -1095,7 +1099,7 @@ class MarkersFinder(Proc):
                 - width (type=int): The width of the plots.
             - order_by: an expression to order the markers, passed by `dplyr::arrange()`.
             - genes: The number of top genes to show or an expression passed to `dplyr::filter()` to filter the genes.
-            - <more>: Other arguments passed to [`scplotter::FeatureStatPlot()`](https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html).
+            - <more>: Other arguments passed to [`biopipen.utils::VizDEGs()`](https://pwwang.github.io/biopipen.utils.R/reference/VizDEGs.html).
         allmarker_plots (type=json): All marker plot cases.
             The keys are the names of the cases and the values are the dicts inherited from `allmarker_plots_defaults`.
         allenrich_plots_defaults (ns): Default options for the plots to generate for the enrichment analysis.
@@ -1110,7 +1114,7 @@ class MarkersFinder(Proc):
             The cases under `envs.cases` can inherit this options.
         marker_plots_defaults (ns): Default options for the plots to generate for the markers.
             - plot_type: The type of the plot.
-                See <https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html>.
+                See <https://pwwang.github.io/biopipen.utils.R/reference/VizDEGs.html>.
                 Available types are `violin`, `box`, `bar`, `ridge`, `dim`, `heatmap` and `dot`.
                 There are two additional types available - `volcano_pct` and `volcano_log2fc`.
             - more_formats (type=list): The extra formats to save the plot in.
@@ -1121,7 +1125,7 @@ class MarkersFinder(Proc):
                 - width (type=int): The width of the plots.
             - order_by: an expression to order the markers, passed by `dplyr::arrange()`.
             - genes: The number of top genes to show or an expression passed to `dplyr::filter()` to filter the genes.
-            - <more>: Other arguments passed to [`scplotter::FeatureStatPlot()`](https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html).
+            - <more>: Other arguments passed to [`biopipen.utils::VizDEGs()`](https://pwwang.github.io/biopipen.utils.R/reference/VizDEGs.html).
                 If `plot_type` is `volcano_pct` or `volcano_log2fc`, they will be passed to
                 [`scplotter::VolcanoPlot()`](https://pwwang.github.io/plotthis/reference/VolcanoPlot.html).
         marker_plots (type=json): Cases of the plots to generate for the markers.

{biopipen-0.34.9 → biopipen-0.34.11}/biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte

@@ -82,6 +82,15 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 </ListItem>
 </UnorderedList>
 
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
+
 {%- macro report_job(job, h=1) -%}
     {{ job | render_job: h=h }}
 {%- endmacro -%}
@@ -92,11 +101,3 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 
 {{ report_jobs(jobs, head_job, report_job) }}
 
-<style>
-.listitem {
-    font-size: large;
-    font-weight: bold;
-    margin: 1rem 0 0.5rem 0;
-    display: inline-block;
-}
-</style>

{biopipen-0.34.9 → biopipen-0.34.11}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.34.9"
+version = "0.34.11"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.34.9 → biopipen-0.34.11}/setup.py

@@ -86,7 +86,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.34.9',
+    'version': '0.34.11',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.34.9/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.34.9"

{biopipen-0.34.9 → biopipen-0.34.11}/biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte

@@ -50,6 +50,15 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 </ListItem>
 </UnorderedList>
 
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
+
 {%- macro report_job(job, h=1) -%}
     {{ job | render_job: h=h }}
 {%- endmacro -%}
@@ -59,12 +68,3 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
-
-<style>
-.listitem {
-    font-size: large;
-    font-weight: bold;
-    margin: 1rem 0 0.5rem 0;
-    display: inline-block;
-}
-</style>

{biopipen-0.34.9 → biopipen-0.34.11}/biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte

@@ -61,6 +61,15 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 </ListItem>
 </UnorderedList>
 
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
+
 {%- macro report_job(job, h=1) -%}
     {{ job | render_job: h=h }}
 {%- endmacro -%}
@@ -70,12 +79,3 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
-
-<style>
-.listitem {
-    font-size: large;
-    font-weight: bold;
-    margin: 1rem 0 0.5rem 0;
-    display: inline-block;
-}
-</style>