Merge pull request #8 from rformassspectrometry/phili

saving and loading of objects
rformassspectrometry · Oct 30, 2024 · c517a01 · c517a01
2 parents b8a51ba + d62b8d2
commit c517a01
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Showing 64 changed files with 300 additions and 351 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,9 +3,12 @@ local_data
 *.o
 *.so
 /.quarto/
+vignettes/.quarto/
 /_site/
 *.html
 *.RData
 *.rmarkdown
 *.js
 *.css
+vignettes/objects/
+man/figures
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metabonaut
 Title: Exploring and Analyzing LC-MS Data
-Version: 0.0.3
+Version: 0.0.4
 Authors@R:
     c(person(given = "Philippine", family = "Louail",
             email = "[email protected]",
@@ -32,6 +32,7 @@ Depends:
     R (>= 4.3),
     BiocParallel (>= 1.8.0)
 Suggests:
+    alabaster.se,
     MsCoreUtils,
     xcms (>= 4.3.4),
     Spectra (>= 1.11.10),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,16 @@
-# metabonaut 0.0
+# metabonaut 0.0.4 
+
+## Changes in 0.0.4
+- Required *alabaster.se*. 
+- In the end-to-end vignette: 
+  - Removal of Spectra data in depth visualisation to 
+    move to the Data investigation vignette 
+  - Removal of internal standard matching to features
+    in the Normalization part. 
+- Save an load *lcms1* and *res* object from the end-to-end workflow 
+  to be used in the Seamless Alignment vignette. Using *MsIO* and 
+  *alabaster.se*
+
 
 ## Changes in 0.0.3
 - Require *xcms* version 4.3.4 and install the package from github.

diff --git a/README.md b/README.md
@@ -1,11 +1,9 @@
 
 
-## Let's explore and learn to analyze untargeted metabolomics data
+# Let's explore and learn to analyze untargeted metabolomics data
 
 [![License: CC BY-NC 4.0](https://img.shields.io/badge/License-CC%20BY--NC%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc/4.0/)
 
-![metabonaut](man/figures/sitcker_small.png)
-
 Welcome to **Metabonaut**! :astronaut:
 
 This initiative presents a series of workflows based on a small LC-MS/MS dataset, 

diff --git a/inst/extdata/preprocessed_lcms1/OBJECT b/inst/extdata/preprocessed_lcms1/OBJECT
@@ -0,0 +1,10 @@
+{
+    "spectra": {
+        "version": "1.0"
+    },
+    "type": "xcms_experiment",
+    "xcms_experiment": {
+        "version": "1.0"
+    }
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/chrom_peak_data/OBJECT b/inst/extdata/preprocessed_lcms1/chrom_peak_data/OBJECT
@@ -0,0 +1,7 @@
+{
+    "data_frame": {
+        "version": "1.0"
+    },
+    "type": "data_frame"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/chrom_peak_data/basic_columns.h5 b/inst/extdata/preprocessed_lcms1/chrom_peak_data/basic_columns.h5
diff --git a/inst/extdata/preprocessed_lcms1/chrom_peaks/OBJECT b/inst/extdata/preprocessed_lcms1/chrom_peaks/OBJECT
@@ -0,0 +1,7 @@
+{
+    "dense_array": {
+        "version": "1.0"
+    },
+    "type": "dense_array"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/chrom_peaks/array.h5 b/inst/extdata/preprocessed_lcms1/chrom_peaks/array.h5
diff --git a/inst/extdata/preprocessed_lcms1/experiment_files/OBJECT b/inst/extdata/preprocessed_lcms1/experiment_files/OBJECT
@@ -0,0 +1,7 @@
+{
+    "spectra": {
+        "version": "1.0"
+    },
+    "type": "ms_experiment_files"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/experiment_files/x/OBJECT b/inst/extdata/preprocessed_lcms1/experiment_files/x/OBJECT
@@ -0,0 +1,8 @@
+{
+    "simple_list": {
+        "version": "1.0",
+        "format": "json.gz"
+    },
+    "type": "simple_list"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/experiment_files/x/list_contents.json.gz b/inst/extdata/preprocessed_lcms1/experiment_files/x/list_contents.json.gz
diff --git a/inst/extdata/preprocessed_lcms1/feature_definitions/OBJECT b/inst/extdata/preprocessed_lcms1/feature_definitions/OBJECT
@@ -0,0 +1,7 @@
+{
+    "data_frame": {
+        "version": "1.0"
+    },
+    "type": "data_frame"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/feature_definitions/basic_columns.h5 b/inst/extdata/preprocessed_lcms1/feature_definitions/basic_columns.h5
diff --git a/inst/extdata/preprocessed_lcms1/feature_definitions/other_columns/10/OBJECT b/inst/extdata/preprocessed_lcms1/feature_definitions/other_columns/10/OBJECT
@@ -0,0 +1,8 @@
+{
+    "simple_list": {
+        "version": "1.0",
+        "format": "json.gz"
+    },
+    "type": "simple_list"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/feature_definitions/other_columns/10/list_contents.json.gz b/inst/extdata/preprocessed_lcms1/feature_definitions/other_columns/10/list_contents.json.gz
diff --git a/inst/extdata/preprocessed_lcms1/metadata/OBJECT b/inst/extdata/preprocessed_lcms1/metadata/OBJECT
@@ -0,0 +1,8 @@
+{
+    "simple_list": {
+        "version": "1.0",
+        "format": "json.gz"
+    },
+    "type": "simple_list"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/metadata/list_contents.json.gz b/inst/extdata/preprocessed_lcms1/metadata/list_contents.json.gz
diff --git a/inst/extdata/preprocessed_lcms1/other_data/OBJECT b/inst/extdata/preprocessed_lcms1/other_data/OBJECT
@@ -0,0 +1,8 @@
+{
+    "simple_list": {
+        "version": "1.0",
+        "format": "json.gz"
+    },
+    "type": "simple_list"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/other_data/list_contents.json.gz b/inst/extdata/preprocessed_lcms1/other_data/list_contents.json.gz
diff --git a/inst/extdata/preprocessed_lcms1/sample_data/OBJECT b/inst/extdata/preprocessed_lcms1/sample_data/OBJECT
@@ -0,0 +1,7 @@
+{
+    "data_frame": {
+        "version": "1.0"
+    },
+    "type": "data_frame"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/sample_data/basic_columns.h5 b/inst/extdata/preprocessed_lcms1/sample_data/basic_columns.h5
diff --git a/inst/extdata/preprocessed_lcms1/sample_data_links/OBJECT b/inst/extdata/preprocessed_lcms1/sample_data_links/OBJECT
@@ -0,0 +1,8 @@
+{
+    "simple_list": {
+        "version": "1.0",
+        "format": "json.gz"
+    },
+    "type": "simple_list"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/sample_data_links/list_contents.json.gz b/inst/extdata/preprocessed_lcms1/sample_data_links/list_contents.json.gz
diff --git a/inst/extdata/preprocessed_lcms1/sample_data_links/other_contents/0/OBJECT b/inst/extdata/preprocessed_lcms1/sample_data_links/other_contents/0/OBJECT
@@ -0,0 +1,7 @@
+{
+    "dense_array": {
+        "version": "1.0"
+    },
+    "type": "dense_array"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/sample_data_links/other_contents/0/array.h5 b/inst/extdata/preprocessed_lcms1/sample_data_links/other_contents/0/array.h5
diff --git a/inst/extdata/preprocessed_lcms1/sample_data_links_mcols/OBJECT b/inst/extdata/preprocessed_lcms1/sample_data_links_mcols/OBJECT
@@ -0,0 +1,7 @@
+{
+    "data_frame": {
+        "version": "1.0"
+    },
+    "type": "data_frame"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/sample_data_links_mcols/basic_columns.h5 b/inst/extdata/preprocessed_lcms1/sample_data_links_mcols/basic_columns.h5
diff --git a/inst/extdata/preprocessed_lcms1/spectra/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/OBJECT
@@ -0,0 +1,7 @@
+{
+    "spectra": {
+        "version": "1.0"
+    },
+    "type": "spectra"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/backend/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/backend/OBJECT
@@ -0,0 +1,7 @@
+{
+    "ms_backend_metabo_lights": {
+        "version": "1.0"
+    },
+    "type": "ms_backend_metabo_lights"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/backend/peaks_variables/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/backend/peaks_variables/OBJECT
@@ -0,0 +1,7 @@
+{
+    "atomic_vector": {
+        "version": "1.0"
+    },
+    "type": "atomic_vector"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/backend/peaks_variables/contents.h5 b/inst/extdata/preprocessed_lcms1/spectra/backend/peaks_variables/contents.h5
diff --git a/inst/extdata/preprocessed_lcms1/spectra/backend/spectra_data/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/backend/spectra_data/OBJECT
@@ -0,0 +1,7 @@
+{
+    "data_frame": {
+        "version": "1.0"
+    },
+    "type": "data_frame"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/backend/spectra_data/basic_columns.h5 b/inst/extdata/preprocessed_lcms1/spectra/backend/spectra_data/basic_columns.h5
diff --git a/inst/extdata/preprocessed_lcms1/spectra/metadata/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/metadata/OBJECT
@@ -0,0 +1,8 @@
+{
+    "simple_list": {
+        "version": "1.0",
+        "format": "json.gz"
+    },
+    "type": "simple_list"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/metadata/list_contents.json.gz b/inst/extdata/preprocessed_lcms1/spectra/metadata/list_contents.json.gz
diff --git a/inst/extdata/preprocessed_lcms1/spectra/processing/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/processing/OBJECT
@@ -0,0 +1,7 @@
+{
+    "atomic_vector": {
+        "version": "1.0"
+    },
+    "type": "atomic_vector"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/processing/contents.h5 b/inst/extdata/preprocessed_lcms1/spectra/processing/contents.h5
diff --git a/inst/extdata/preprocessed_lcms1/spectra/processing_chunk_size/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/processing_chunk_size/OBJECT
@@ -0,0 +1,7 @@
+{
+    "atomic_vector": {
+        "version": "1.0"
+    },
+    "type": "atomic_vector"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/processing_chunk_size/contents.h5 b/inst/extdata/preprocessed_lcms1/spectra/processing_chunk_size/contents.h5
diff --git a/inst/extdata/preprocessed_lcms1/spectra/processing_queue_variables/OBJECT b/inst/extdata/preprocessed_lcms1/spectra/processing_queue_variables/OBJECT
@@ -0,0 +1,7 @@
+{
+    "atomic_vector": {
+        "version": "1.0"
+    },
+    "type": "atomic_vector"
+}
+
diff --git a/inst/extdata/preprocessed_lcms1/spectra/processing_queue_variables/contents.h5 b/inst/extdata/preprocessed_lcms1/spectra/processing_queue_variables/contents.h5
diff --git a/inst/extdata/preprocessed_lcms1/spectra/spectra_processing_queue.json b/inst/extdata/preprocessed_lcms1/spectra/spectra_processing_queue.json
@@ -0,0 +1 @@
+["{\"type\":\"list\",\"attributes\":{},\"value\":[]}"]
diff --git a/inst/extdata/preprocessed_lcms1/xcms_experiment_process_history.json b/inst/extdata/preprocessed_lcms1/xcms_experiment_process_history.json
diff --git a/inst/extdata/preprocessed_res/OBJECT b/inst/extdata/preprocessed_res/OBJECT
@@ -0,0 +1,11 @@
+{
+    "summarized_experiment": {
+        "version": "1.0",
+        "dimensions": [
+            9068,
+            10
+        ]
+    },
+    "type": "summarized_experiment"
+}
+
diff --git a/inst/extdata/preprocessed_res/assays/0/OBJECT b/inst/extdata/preprocessed_res/assays/0/OBJECT
@@ -0,0 +1,7 @@
+{
+    "dense_array": {
+        "version": "1.0"
+    },
+    "type": "dense_array"
+}
+
diff --git a/inst/extdata/preprocessed_res/assays/0/array.h5 b/inst/extdata/preprocessed_res/assays/0/array.h5
diff --git a/inst/extdata/preprocessed_res/assays/1/OBJECT b/inst/extdata/preprocessed_res/assays/1/OBJECT
@@ -0,0 +1,7 @@
+{
+    "dense_array": {
+        "version": "1.0"
+    },
+    "type": "dense_array"
+}
+
diff --git a/inst/extdata/preprocessed_res/assays/1/array.h5 b/inst/extdata/preprocessed_res/assays/1/array.h5
diff --git a/inst/extdata/preprocessed_res/assays/names.json b/inst/extdata/preprocessed_res/assays/names.json
@@ -0,0 +1 @@
+["raw","raw_filled"]
diff --git a/inst/extdata/preprocessed_res/column_data/OBJECT b/inst/extdata/preprocessed_res/column_data/OBJECT
@@ -0,0 +1,7 @@
+{
+    "data_frame": {
+        "version": "1.0"
+    },
+    "type": "data_frame"
+}
+
diff --git a/inst/extdata/preprocessed_res/column_data/basic_columns.h5 b/inst/extdata/preprocessed_res/column_data/basic_columns.h5
diff --git a/inst/extdata/preprocessed_res/row_data/OBJECT b/inst/extdata/preprocessed_res/row_data/OBJECT
@@ -0,0 +1,7 @@
+{
+    "data_frame": {
+        "version": "1.0"
+    },
+    "type": "data_frame"
+}
+
diff --git a/inst/extdata/preprocessed_res/row_data/basic_columns.h5 b/inst/extdata/preprocessed_res/row_data/basic_columns.h5
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diff --git a/pkgdown/favicon/site.webmanifest b/pkgdown/favicon/site.webmanifest
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