From 06e09ee37f7b1e60750efa66da651ebffe235419 Mon Sep 17 00:00:00 2001 From: kennyAgricultureVic Date: Mon, 23 Dec 2024 16:24:58 +1100 Subject: [PATCH 1/2] Add index page placeholders for Basic Functions, Use Cases, and User Stories; update mkdocs.yml navigation --- docs/Basic-Functions/index.md | 2 ++ docs/Use-Cases/index.md | 1 + docs/User-Stories/index.md | 1 + mkdocs.yml | 3 +++ 4 files changed, 7 insertions(+) create mode 100644 docs/Basic-Functions/index.md create mode 100644 docs/Use-Cases/index.md create mode 100644 docs/User-Stories/index.md diff --git a/docs/Basic-Functions/index.md b/docs/Basic-Functions/index.md new file mode 100644 index 0000000..b889eaa --- /dev/null +++ b/docs/Basic-Functions/index.md @@ -0,0 +1,2 @@ +# Basic Functions + diff --git a/docs/Use-Cases/index.md b/docs/Use-Cases/index.md new file mode 100644 index 0000000..9ec7aa2 --- /dev/null +++ b/docs/Use-Cases/index.md @@ -0,0 +1 @@ +# Use Cases \ No newline at end of file diff --git a/docs/User-Stories/index.md b/docs/User-Stories/index.md new file mode 100644 index 0000000..5fc1ebe --- /dev/null +++ b/docs/User-Stories/index.md @@ -0,0 +1 @@ +# User Stories \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 44bc787..c678e12 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -30,15 +30,18 @@ nav: - About Pretzel: - index.md - User Stories: + - User-Stories/index.md - User-Stories/User-story-1.md - User-Stories/User-story-2.md - User-Stories/User-story-3.md - Use Cases: + - Use-Cases/index.md - Use-Cases/Finding-a-marker-or-gene-on-a-genome.md - Use-Cases/Visualise-genotype-data-for-a-subset-of-accessions-around-specific-genomic-regions.md - Use-Cases/Visualise-the-location-of-a-subset-of-markers.md - Use-Cases/VCF-genotype-search.md - Basic Functions: + - Basic-Functions/index.md - Basic-Functions/Search-tab.md - Basic-Functions/Features-tab.md - Basic-Functions/Adding-and-removing-datasets-from-the-view.md From abca396547ff48756342196b02b1ca952401db65 Mon Sep 17 00:00:00 2001 From: kennyAgricultureVic Date: Mon, 23 Dec 2024 20:23:30 +1100 Subject: [PATCH 2/2] Removal of notes used when testing VCF genotype search. Formatting update for feature names --- docs/Use-Cases/VCF-genotype-search.md | 14 ++++---------- ...isualise-the-location-of-a-subset-of-markers.md | 7 ++++--- 2 files changed, 8 insertions(+), 13 deletions(-) diff --git a/docs/Use-Cases/VCF-genotype-search.md b/docs/Use-Cases/VCF-genotype-search.md index 713b650..b9be224 100644 --- a/docs/Use-Cases/VCF-genotype-search.md +++ b/docs/Use-Cases/VCF-genotype-search.md @@ -3,13 +3,6 @@ In this Use Case, a summary of genotypes for AGG Plant Genetic Resources can be simply and rapidly visualised. For example, a user may wish to view the genotypes for a set of accessions of interest at a small subset of trait linked markers, to make a decision on which accessions to use in an experiment. In this example we will use Pretzel to display a summary of a set of AGG barley Plant Genetic Resources at two markers AVRIG00246 and AVRIG00484. -!!! note - - The following feature is currently being developed. Please access it at [https://dev.plantinformatics.io/login](https://dev.plantinformatics.io/login) using the following login credentials. - Username: test@test - Password: test - - ![vcf-feature-search](https://github.com/user-attachments/assets/f29743ac-29ff-4660-a384-5991cc48028c) ## Loading a VCF and selecting samples @@ -31,9 +24,10 @@ To select a range of samples, hold down the CRTL key and select another sample i ## Adding features to be searched Within the Features input text box, paste your feature IDs. The one used in this example is: - - AVRIG00246 - AVRIG00484 +``` text title="Feature names" +AVRIG00246 +AVRIG00484 +``` ![vcf-feature-search-05](https://github.com/user-attachments/assets/a914dd99-83eb-421e-b5cf-c6a17d36abb9) ## End output ![vcf-feature-search-06](https://github.com/user-attachments/assets/44b9ca10-cb88-4342-b5ef-06ac47faf054) diff --git a/docs/Use-Cases/Visualise-the-location-of-a-subset-of-markers.md b/docs/Use-Cases/Visualise-the-location-of-a-subset-of-markers.md index e7e67b3..340f81a 100644 --- a/docs/Use-Cases/Visualise-the-location-of-a-subset-of-markers.md +++ b/docs/Use-Cases/Visualise-the-location-of-a-subset-of-markers.md @@ -5,9 +5,10 @@ Click on the "Search" button the left hand search panel ![enter image description here](https://pretzel-images-public.s3.ap-southeast-2.amazonaws.com/use-case/visualise-subset-of-markers%E2%80%8B/sm-1.png) Enter the a list of feature names into the search text box input and press the search button - - AVRIG00246 - AVRIG00484 +``` text title="Feature names" +AVRIG00246 +AVRIG00484 +``` ![enter image description here](https://pretzel-images-public.s3.ap-southeast-2.amazonaws.com/use-case/visualise-subset-of-markers%E2%80%8B/sm-2.png)