biopipen 0.34.9__py3-none-any.whl → 0.34.11__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.34.9"
+__version__ = "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/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/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/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>

{biopipen-0.34.9.dist-info → biopipen-0.34.11.dist-info}/METADATA

@@ -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-0.34.9.dist-info → biopipen-0.34.11.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=zx5DRdGvH-gZCcW6m_sgJE0BiH5pc_-kR07ANPXxh70,23
+biopipen/__init__.py,sha256=1GTRPz3gyaWKOyHElhtx6TB-YNqMbOWmaezYgfEjQI0,24
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
@@ -22,7 +22,7 @@ biopipen/ns/plot.py,sha256=N41_izb6zi-XArUly5WhLebapNXbTNSgGlOCCwtrDlY,18282
 biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
 biopipen/ns/regulatory.py,sha256=WlnX_R8jEFyxCjk8mru5Qu5iCQJLzjMWiWGoc3gygzc,16221
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=-pW0noyhqocHwoN4mF6ZYegfryc5H_l4AB53EQ2e-UE,146055
+biopipen/ns/scrna.py,sha256=i3LNPJtr3qZeweMnp7Z4x31oRYwkp6KsQrst4epOWEU,146288
 biopipen/ns/scrna_metabolic_landscape.py,sha256=EwLMrsj_pTqvyAgtHLoishjQxCg_j8n5OofuTofUph0,22096
 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
@@ -51,9 +51,9 @@ biopipen/reports/scrna/DimPlots.svelte,sha256=ubIx8dgppzSB8WS_B4LN2T3bOTerP4Ck6o
 biopipen/reports/scrna/MarkersFinder.svelte,sha256=77rD1psj0VJykPDhfwS-B8mubvaasREAE6RYR2atTN4,444
 biopipen/reports/scrna/MetaMarkers.svelte,sha256=iIFRKjvVYrM1AtDWqq8UfeS8q23R8FKg2yepKAw2KSE,508
 biopipen/reports/scrna/RadarPlots.svelte,sha256=g_fp9d3vdnzk-egXPhkhhfWXOeG569Rj8rYLRIKmlLc,396
-biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=0AmtzoGZXh5OnxGtZd5NBItVd-BeuGk9mEIhhWa1ab8,2527
-biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=RpIT1O3yiJEEqRcdS-ydYDghChQ0YLbD1RtSK2CQS_k,5654
-biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=kW6AxFr7VnX9yVL74IbUEBuI7xRfbmnROXR6C7jRets,3009
+biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=4ruKluhHiKG1_sLnkCddYWIeVGXN6uzL_k2yl3jsS8k,2527
+biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=nA35qYGDGdeFcMLqrP_T5VDpFKIA_p3wrnhiMQXlPLQ,5655
+biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=hSVrDzVo1vEIh2XQTFL36hBpg_VCObXwKzeaCTZRWUU,3009
 biopipen/reports/snp/PlinkCallRate.svelte,sha256=u0JGUzBS6MJR38TrI7tz08E7uFJToFPeALinu-KLUOg,706
 biopipen/reports/snp/PlinkFreq.svelte,sha256=GCLQXL3OY4b8BDzaLZ3vHVrsv2lNm5657UaSdiimE9w,523
 biopipen/reports/snp/PlinkHWE.svelte,sha256=zlAbn0DLwGBka-X9-MQplpfYkQIanH-QhgQL2GtK0UA,490
@@ -284,7 +284,7 @@ biopipen/utils/misc.py,sha256=pDZ-INWVNqHuXYvcjmu8KqNAigkh2lsHy0BxX44CPvc,4048
 biopipen/utils/reference.py,sha256=Oc6IlA1giLxymAuI7DO-IQLHQ7-DbsWzOQE86oTDfMU,5955
 biopipen/utils/reporter.py,sha256=VwLl6xyVDWnGY7NEXyqBlkW8expKJoNQ5iTyZSELf5c,4922
 biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
-biopipen-0.34.9.dist-info/METADATA,sha256=aYXqI1hITAFJ1bhVKyz2toplmcj0oNdfKqa3JU-poBw,1026
-biopipen-0.34.9.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-biopipen-0.34.9.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.34.9.dist-info/RECORD,,
+biopipen-0.34.11.dist-info/METADATA,sha256=MfIYyJ_H0P5vB0uzbCXpFQsDQ4hBAHPV-lrk-IBAAH0,1027
+biopipen-0.34.11.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+biopipen-0.34.11.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.34.11.dist-info/RECORD,,