lightning.git
7 months ago20461 Updating README 20461-updating-gvcf
Alex Coleman [Wed, 20 Sep 2023 16:23:44 +0000 (10:23 -0600)]
20461 Updating README

Updating dockerfile paths in README.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

7 months ago20461: Updating main workflow and README.md
Alex Coleman [Thu, 14 Sep 2023 16:54:36 +0000 (10:54 -0600)]
20461: Updating main workflow and README.md

Updating main workflow to call scatter workflows, and adding some more info to README.md

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

8 months ago20461 updating resource requirements
Alex Coleman [Tue, 22 Aug 2023 18:38:13 +0000 (12:38 -0600)]
20461 updating resource requirements

Updating resource requirements for helper CWL.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

8 months ago20461: Updating workflow and README.
Alex Coleman [Tue, 22 Aug 2023 16:35:47 +0000 (10:35 -0600)]
20461: Updating workflow and README.

Making documentation changes to readme, and fixing sampleid issue for workflow.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months ago20461: Updating to support multiple possible types of sample-id input.
Alex Coleman [Mon, 31 Jul 2023 18:01:53 +0000 (12:01 -0600)]
20461: Updating to support multiple possible types of sample-id input.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoAdding copyright headers.
Alex Coleman [Fri, 14 Jul 2023 16:29:44 +0000 (10:29 -0600)]
Adding copyright headers.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoUpdating README.md to further explain different inputs.
Alex Coleman [Thu, 13 Jul 2023 18:55:09 +0000 (12:55 -0600)]
Updating README.md to further explain different inputs.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoUpdating README to better describe what inputs are required for different subworkflows.
Alex Coleman [Fri, 30 Jun 2023 16:12:36 +0000 (10:12 -0600)]
Updating README to better describe what inputs are required for different subworkflows.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoUpdating main workflow for appropriate conditional logic.
acoleman2000 [Mon, 26 Jun 2023 21:38:44 +0000 (15:38 -0600)]
Updating main workflow for appropriate conditional logic.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoUpdating main workflow to add spacing.
acoleman2000 [Wed, 21 Jun 2023 16:30:42 +0000 (10:30 -0600)]
Updating main workflow to add spacing.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoUpdating workflow so scatter that occurs before conditional evalution occurs without...
acoleman2000 [Fri, 16 Jun 2023 21:17:43 +0000 (15:17 -0600)]
Updating workflow so scatter that occurs before conditional evalution occurs without errors (setting default to be [])
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoUpdating Dockerfile for vcfutil to point to my gvcf repo with updated changes for...
acoleman2000 [Fri, 16 Jun 2023 16:58:06 +0000 (10:58 -0600)]
Updating Dockerfile for vcfutil to point to my gvcf repo with updated changes for .gz files, and proper base image.
Updating workflow to support EITHER list of vcf files OR directory of vcf files to be provided. Adding more conditional logic for workflows.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>.

9 months agoUpdating README.md.
acoleman2000 [Wed, 7 Jun 2023 16:55:57 +0000 (10:55 -0600)]
Updating README.md.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

9 months agoRemoving files (moved to subdirs) and updating main wf.
acoleman2000 [Fri, 12 May 2023 18:25:56 +0000 (14:25 -0400)]
Removing files (moved to subdirs) and updating main wf.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>.

9 months agoOrganizing cwl files and creating conditional workflow.
acoleman2000 [Fri, 12 May 2023 18:19:49 +0000 (14:19 -0400)]
Organizing cwl files and creating conditional workflow.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>.

9 months agoAdding README.md.
acoleman2000 [Thu, 4 May 2023 15:33:51 +0000 (11:33 -0400)]
Adding README.md.
Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

13 months agoMerge branch '19995-glm-freq-threshold'
Tom Clegg [Tue, 7 Mar 2023 04:46:39 +0000 (23:46 -0500)]
Merge branch '19995-glm-freq-threshold'

refs #19995

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

13 months ago19995: Skip GLM on variants below frequency threshold.
Tom Clegg [Mon, 6 Mar 2023 16:21:25 +0000 (11:21 -0500)]
19995: Skip GLM on variants below frequency threshold.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoMerge branch '19997-glm'
Tom Clegg [Thu, 2 Feb 2023 17:02:25 +0000 (12:02 -0500)]
Merge branch '19997-glm'

refs #19997

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoPreserve pca components from input when writing samples.csv.
Tom Clegg [Thu, 2 Feb 2023 16:10:13 +0000 (11:10 -0500)]
Preserve pca components from input when writing samples.csv.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoFix validation=0 in samples.csv (should be empty for non-c/c).
Tom Clegg [Thu, 2 Feb 2023 15:00:12 +0000 (10:00 -0500)]
Fix validation=0 in samples.csv (should be empty for non-c/c).

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoTurn off auto-retry.
Tom Clegg [Thu, 2 Feb 2023 15:00:01 +0000 (10:00 -0500)]
Turn off auto-retry.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

15 months agoMerge branch '19868-pca-in-ml' into main
Jiayong Li [Fri, 27 Jan 2023 19:39:13 +0000 (19:39 +0000)]
Merge branch '19868-pca-in-ml' into main

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoMerge branch 'main' into 19868-pca-in-ml 19868-pca-in-ml
Jiayong Li [Fri, 27 Jan 2023 19:38:44 +0000 (19:38 +0000)]
Merge branch 'main' into 19868-pca-in-ml

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoChange resource requirement of gvcf2fasta and imputation
Jiayong Li [Fri, 27 Jan 2023 19:37:08 +0000 (19:37 +0000)]
Change resource requirement of gvcf2fasta and imputation

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoDarker colors.
Tom Clegg [Fri, 20 Jan 2023 19:25:02 +0000 (14:25 -0500)]
Darker colors.

refs #19958

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

15 months agoBring back genomewideline/suggestiveline options.
Tom Clegg [Fri, 20 Jan 2023 18:37:34 +0000 (13:37 -0500)]
Bring back genomewideline/suggestiveline options.

refs #19958

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

15 months agoMerge branch '19868-pca-in-ml' into main
Jiayong Li [Fri, 20 Jan 2023 14:38:41 +0000 (14:38 +0000)]
Merge branch '19868-pca-in-ml' into main

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoMerge branch 'main' into 19868-pca-in-ml
Jiayong Li [Fri, 20 Jan 2023 14:37:58 +0000 (14:37 +0000)]
Merge branch 'main' into 19868-pca-in-ml

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoChange slice-numpy-onehot parameter
Jiayong Li [Fri, 20 Jan 2023 14:36:55 +0000 (14:36 +0000)]
Change slice-numpy-onehot parameter

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoGenerate a manhattan plot for each chromosome.
Tom Clegg [Thu, 19 Jan 2023 21:38:41 +0000 (16:38 -0500)]
Generate a manhattan plot for each chromosome.

refs #19958

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

15 months agoFix GLM p-value calculation when -case-control-only=true.
Tom Clegg [Fri, 13 Jan 2023 20:05:27 +0000 (15:05 -0500)]
Fix GLM p-value calculation when -case-control-only=true.

refs #19566

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

15 months agoMerge branch '19868-pca-in-ml' into main
Jiayong Li [Thu, 12 Jan 2023 16:18:07 +0000 (16:18 +0000)]
Merge branch '19868-pca-in-ml' into main

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoMerge branch 'main' into 19868-pca-in-ml
Jiayong Li [Thu, 12 Jan 2023 16:17:19 +0000 (16:17 +0000)]
Merge branch 'main' into 19868-pca-in-ml

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoFix shebang and license
Jiayong Li [Thu, 12 Jan 2023 16:07:42 +0000 (16:07 +0000)]
Fix shebang and license

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

15 months agoFix -min-coverage calculation broken when -case-control-only=true.
Tom Clegg [Tue, 10 Jan 2023 15:00:16 +0000 (10:00 -0500)]
Fix -min-coverage calculation broken when -case-control-only=true.

refs #19868

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

15 months agoAdd column headings to slice-numpy -pca sample list output.
Tom Clegg [Tue, 3 Jan 2023 21:29:12 +0000 (16:29 -0500)]
Add column headings to slice-numpy -pca sample list output.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

15 months agoFix validation flag in slice-numpy -pca sample list output.
Tom Clegg [Tue, 3 Jan 2023 21:23:05 +0000 (16:23 -0500)]
Fix validation flag in slice-numpy -pca sample list output.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months agoMerge branch '19526-manhattan-plot'
Tom Clegg [Wed, 21 Dec 2022 19:46:20 +0000 (14:46 -0500)]
Merge branch '19526-manhattan-plot'

refs #19526

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19526: Output tile locations and pvalues at specified threshold. 19526-manhattan-plot
Tom Clegg [Mon, 19 Dec 2022 21:51:02 +0000 (16:51 -0500)]
19526: Output tile locations and pvalues at specified threshold.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months agoMerge branch '19566-glm'
Tom Clegg [Mon, 19 Dec 2022 19:25:54 +0000 (14:25 -0500)]
Merge branch '19566-glm'

refs #19566

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Preemptible flag.
Tom Clegg [Mon, 19 Dec 2022 19:22:34 +0000 (14:22 -0500)]
19566: Preemptible flag.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Record number of p-value calculations performed.
Tom Clegg [Mon, 19 Dec 2022 15:10:16 +0000 (10:10 -0500)]
19566: Record number of p-value calculations performed.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Silence logging from glm library. 19566-glm
Tom Clegg [Fri, 16 Dec 2022 19:25:12 +0000 (14:25 -0500)]
19566: Silence logging from glm library.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Fix chi2 used instead of logistic regression p-value.
Tom Clegg [Fri, 16 Dec 2022 15:45:25 +0000 (10:45 -0500)]
19566: Fix chi2 used instead of logistic regression p-value.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months agoMerge branch '19785-add-cwl' into main
Jiayong Li [Thu, 15 Dec 2022 22:21:02 +0000 (22:21 +0000)]
Merge branch '19785-add-cwl' into main

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

16 months agoMerge branch 'main' into 19785-add-cwl 19785-add-cwl
Jiayong Li [Thu, 15 Dec 2022 22:20:16 +0000 (22:20 +0000)]
Merge branch 'main' into 19785-add-cwl

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

16 months agoChange lightning docker file so that it builds the current branch instead of main
Jiayong Li [Thu, 15 Dec 2022 22:15:13 +0000 (22:15 +0000)]
Change lightning docker file so that it builds the current branch instead of main

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

16 months ago19566: Merge branch 'main'
Tom Clegg [Thu, 15 Dec 2022 15:59:27 +0000 (10:59 -0500)]
19566: Merge branch 'main'

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months agoMerge branch '19526-manhattan-plot'
Tom Clegg [Thu, 15 Dec 2022 15:59:03 +0000 (10:59 -0500)]
Merge branch '19526-manhattan-plot'

refs #19526

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Precompute cov glm.
Tom Clegg [Wed, 14 Dec 2022 20:00:46 +0000 (15:00 -0500)]
19566: Precompute cov glm.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months agoMerge branch '19566-glm'
Tom Clegg [Tue, 13 Dec 2022 15:03:06 +0000 (10:03 -0500)]
Merge branch '19566-glm'

refs #19566

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Test p-value vs. Python.
Tom Clegg [Mon, 12 Dec 2022 16:37:21 +0000 (11:37 -0500)]
19566: Test p-value vs. Python.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Normalize pca values before glm.
Tom Clegg [Fri, 2 Dec 2022 19:23:34 +0000 (14:23 -0500)]
19566: Normalize pca values before glm.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months ago19566: Add constant, check GLM results against Python.
Tom Clegg [Fri, 2 Dec 2022 18:59:29 +0000 (13:59 -0500)]
19566: Add constant, check GLM results against Python.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

16 months agoMerge branch '19785-add-cwl' into main
Jiayong Li [Fri, 9 Dec 2022 21:09:17 +0000 (21:09 +0000)]
Merge branch '19785-add-cwl' into main

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

16 months agoFix readme
Jiayong Li [Fri, 9 Dec 2022 21:08:35 +0000 (21:08 +0000)]
Fix readme

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

16 months agoMerge branch '19785-add-cwl' into main
Jiayong Li [Fri, 9 Dec 2022 21:05:32 +0000 (21:05 +0000)]
Merge branch '19785-add-cwl' into main

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

16 months agoAdd cwl and docker files
Jiayong Li [Fri, 9 Dec 2022 21:03:13 +0000 (21:03 +0000)]
Add cwl and docker files

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

16 months ago19526: Tidy manhattan plot.
Tom Clegg [Thu, 1 Dec 2022 18:13:18 +0000 (13:13 -0500)]
19526: Tidy manhattan plot.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19566: Option to limit pca components used in glm. Fix onehot use.
Tom Clegg [Tue, 29 Nov 2022 16:22:12 +0000 (11:22 -0500)]
19566: Option to limit pca components used in glm. Fix onehot use.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19566: glm one column at a time.
Tom Clegg [Tue, 29 Nov 2022 16:10:32 +0000 (11:10 -0500)]
19566: glm one column at a time.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19566: Logistic regression p-value.
Tom Clegg [Tue, 29 Nov 2022 15:43:29 +0000 (10:43 -0500)]
19566: Logistic regression p-value.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months agoMerge branch '19526-manhattan-plot'
Tom Clegg [Mon, 28 Nov 2022 20:18:32 +0000 (15:18 -0500)]
Merge branch '19526-manhattan-plot'

refs #19526

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19526: Add manhattan plot.
Tom Clegg [Mon, 28 Nov 2022 18:34:48 +0000 (13:34 -0500)]
19526: Add manhattan plot.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months agoCheck for unparsed command line args.
Tom Clegg [Fri, 18 Nov 2022 18:28:36 +0000 (13:28 -0500)]
Check for unparsed command line args.

refs #19780

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19780: Fix indexing error.
Tom Clegg [Fri, 18 Nov 2022 17:50:49 +0000 (12:50 -0500)]
19780: Fix indexing error.

refs #19780

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: slice-numpy accepts samples.csv with or without p-values.
Tom Clegg [Wed, 16 Nov 2022 20:22:55 +0000 (15:22 -0500)]
19527: slice-numpy accepts samples.csv with or without p-values.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Update arvados sdk.
Tom Clegg [Mon, 14 Nov 2022 00:06:41 +0000 (19:06 -0500)]
19527: Update arvados sdk.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Fix odd # columns to pca.
Tom Clegg [Fri, 11 Nov 2022 21:04:54 +0000 (16:04 -0500)]
19527: Fix odd # columns to pca.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Fix one-hot matrix.
Tom Clegg [Fri, 11 Nov 2022 17:44:16 +0000 (12:44 -0500)]
19527: Fix one-hot matrix.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Enable choose-samples to work without case/control info.
Tom Clegg [Fri, 11 Nov 2022 17:35:09 +0000 (12:35 -0500)]
19527: Enable choose-samples to work without case/control info.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Fix Χ² calculation.
Tom Clegg [Fri, 11 Nov 2022 01:55:11 +0000 (20:55 -0500)]
19527: Fix Χ² calculation.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Output samples.csv earlier.
Tom Clegg [Thu, 10 Nov 2022 20:49:35 +0000 (15:49 -0500)]
19527: Output samples.csv earlier.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Fix crash on tag skipped for min-coverage.
Tom Clegg [Thu, 10 Nov 2022 19:40:45 +0000 (14:40 -0500)]
19527: Fix crash on tag skipped for min-coverage.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Option to exclude non-case/control samples.
Tom Clegg [Thu, 10 Nov 2022 16:16:59 +0000 (11:16 -0500)]
19527: Option to exclude non-case/control samples.

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months agoMerge branch '19527-training-set'
Tom Clegg [Thu, 10 Nov 2022 15:24:53 +0000 (10:24 -0500)]
Merge branch '19527-training-set'

refs #19527

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Accommodate header row in samples csv. 19527-training-set
Tom Clegg [Wed, 9 Nov 2022 23:29:58 +0000 (18:29 -0500)]
19527: Accommodate header row in samples csv.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Ignore empty line at EOF.
Tom Clegg [Wed, 9 Nov 2022 23:08:57 +0000 (18:08 -0500)]
19527: Ignore empty line at EOF.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months agoMerge branch '19524-pca'
Tom Clegg [Wed, 9 Nov 2022 20:12:33 +0000 (15:12 -0500)]
Merge branch '19524-pca'

refs #19524

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Fix p-value calculation.
Tom Clegg [Wed, 9 Nov 2022 20:11:48 +0000 (15:11 -0500)]
19527: Fix p-value calculation.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Load training-set flag from samples.csv.
Tom Clegg [Wed, 9 Nov 2022 19:39:31 +0000 (14:39 -0500)]
19527: Load training-set flag from samples.csv.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: choose-samples: training/validation set.
Tom Clegg [Mon, 7 Nov 2022 14:29:47 +0000 (09:29 -0500)]
19527: choose-samples: training/validation set.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19527: Load training-set flag from samples.csv.
Tom Clegg [Wed, 9 Nov 2022 19:24:49 +0000 (14:24 -0500)]
19527: Load training-set flag from samples.csv.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months agochoose-samples: training/validation set.
Tom Clegg [Mon, 7 Nov 2022 14:29:47 +0000 (09:29 -0500)]
choose-samples: training/validation set.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months ago19524: Fit PCA to specified training set.
Tom Clegg [Wed, 2 Nov 2022 14:49:09 +0000 (10:49 -0400)]
19524: Fit PCA to specified training set.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

17 months agoMerge branch '19524-pca'
Tom Clegg [Mon, 31 Oct 2022 15:53:26 +0000 (11:53 -0400)]
Merge branch '19524-pca'

refs #19524

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Fix matrix alloc size. 19524-pca
Tom Clegg [Fri, 21 Oct 2022 13:23:12 +0000 (09:23 -0400)]
19524: Fix matrix alloc size.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Flags choose which PCA components to plot.
Tom Clegg [Thu, 20 Oct 2022 17:06:35 +0000 (13:06 -0400)]
19524: Flags choose which PCA components to plot.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Update colors, plot unknown-phenotype behind known.
Tom Clegg [Thu, 20 Oct 2022 15:23:08 +0000 (11:23 -0400)]
19524: Update colors, plot unknown-phenotype behind known.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Limit size of PCA input matrix.
Tom Clegg [Thu, 20 Oct 2022 14:07:11 +0000 (10:07 -0400)]
19524: Limit size of PCA input matrix.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Limit size of PCA input matrix.
Tom Clegg [Wed, 19 Oct 2022 20:17:36 +0000 (16:17 -0400)]
19524: Limit size of PCA input matrix.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: configurable vcpus/ram
Tom Clegg [Wed, 19 Oct 2022 19:55:56 +0000 (15:55 -0400)]
19524: configurable vcpus/ram

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months agoMerge branch '19524-pca'
Tom Clegg [Fri, 14 Oct 2022 17:34:23 +0000 (13:34 -0400)]
Merge branch '19524-pca'

refs #19524

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Use marker shape to indicate second category variable.
Tom Clegg [Thu, 13 Oct 2022 18:46:46 +0000 (14:46 -0400)]
19524: Use marker shape to indicate second category variable.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Remove obsolete pca cmds.
Tom Clegg [Thu, 13 Oct 2022 15:44:05 +0000 (11:44 -0400)]
19524: Remove obsolete pca cmds.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Fix deprecated scipy.load.
Tom Clegg [Thu, 13 Oct 2022 14:47:51 +0000 (10:47 -0400)]
19524: Fix deprecated scipy.load.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Read multiple phenotype files.
Tom Clegg [Thu, 13 Oct 2022 14:47:02 +0000 (10:47 -0400)]
19524: Read multiple phenotype files.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months ago19524: Generalize plot colors a little.
Tom Clegg [Thu, 13 Oct 2022 14:43:36 +0000 (10:43 -0400)]
19524: Generalize plot colors a little.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

18 months agoFail if inadvertently using randomness.
Tom Clegg [Thu, 13 Oct 2022 13:57:37 +0000 (09:57 -0400)]
Fail if inadvertently using randomness.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>