lightning.git
18 months agoFix missing struct field.
Tom Clegg [Mon, 26 Jun 2023 14:32:03 +0000 (10:32 -0400)]
Fix missing struct field.

refs #19995

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

19 months agoMerge branch '19995-glm-freq-threshold'
Tom Clegg [Fri, 5 May 2023 19:10:32 +0000 (15:10 -0400)]
Merge branch '19995-glm-freq-threshold'

refs #19995
refs #20233

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

20 months ago19995: Add -max-frequency filter. 19995-glm-freq-threshold
Tom Clegg [Thu, 6 Apr 2023 19:53:31 +0000 (15:53 -0400)]
19995: Add -max-frequency filter.

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

20 months ago19995: Report MAF in onehot-columns.npy.
Tom Clegg [Wed, 29 Mar 2023 20:29:19 +0000 (16:29 -0400)]
19995: Report MAF in onehot-columns.npy.

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

20 months ago19995: Use allele frequency, apply min freq cutoff to Χ² pvalue too.
Tom Clegg [Wed, 29 Mar 2023 15:56:42 +0000 (11:56 -0400)]
19995: Use allele frequency, apply min freq cutoff to Χ² pvalue too.

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

21 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>

21 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>

22 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>

22 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>

22 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>

22 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>

22 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>

22 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>

22 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years 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>

2 years ago19524: Fix colormap.
Tom Clegg [Wed, 12 Oct 2022 18:36:33 +0000 (14:36 -0400)]
19524: Fix colormap.

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

2 years ago19524: propagate pca-components arg.
Tom Clegg [Wed, 12 Oct 2022 05:11:26 +0000 (01:11 -0400)]
19524: propagate pca-components arg.

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

2 years ago19524: plot: get sample list from csv instead of fasta filenames.
Tom Clegg [Tue, 11 Oct 2022 18:40:03 +0000 (14:40 -0400)]
19524: plot: get sample list from csv instead of fasta filenames.

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

2 years ago19524: Output PCA.
Tom Clegg [Tue, 11 Oct 2022 14:07:14 +0000 (10:07 -0400)]
19524: Output PCA.

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

2 years agoUpdate deps, improve error reporting
Tom Clegg [Fri, 7 Oct 2022 19:18:39 +0000 (15:18 -0400)]
Update deps, improve error reporting

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

2 years agoUse min-coverage filter
Tom Clegg [Fri, 7 Oct 2022 18:11:31 +0000 (14:11 -0400)]
Use min-coverage filter

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

2 years agoFix diff case
Tom Clegg [Fri, 5 Aug 2022 19:45:52 +0000 (15:45 -0400)]
Fix diff case

refs #19236 #note-20

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

2 years agoFix diff case
Tom Clegg [Wed, 3 Aug 2022 20:14:27 +0000 (16:14 -0400)]
Fix diff case

refs #19236 #note-15.7

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

2 years agoFix diff case
Tom Clegg [Wed, 27 Jul 2022 20:56:09 +0000 (16:56 -0400)]
Fix diff case

refs #19236 #note-15.6

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

2 years agoFix diff case
Tom Clegg [Wed, 27 Jul 2022 20:02:40 +0000 (16:02 -0400)]
Fix diff case

refs #19236 #note-15.4, #note-15.5

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

2 years agoFix diff case
Tom Clegg [Wed, 27 Jul 2022 18:48:05 +0000 (14:48 -0400)]
Fix diff case

refs #19236 #note-15.2, #note-15.3

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