From 0dde6198d5c152f68ef5032db71fac64796e7e48 Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 7 Oct 2020 10:49:11 +0200 Subject: [PATCH 1/5] Fix the XLSX use in docs (XLSX was removed from GigaSOM imports) --- docs/src/tutorials/processingFCSData.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/src/tutorials/processingFCSData.md b/docs/src/tutorials/processingFCSData.md index 18046acc..775a472d 100644 --- a/docs/src/tutorials/processingFCSData.md +++ b/docs/src/tutorials/processingFCSData.md @@ -160,8 +160,9 @@ extract information about FCS data columns from there. First, we read the actual content using the XLSX package: ```julia -md = GigaSOM.DataFrame(GigaSOM.XLSX.readtable("PBMC8_metadata.xlsx", "Sheet1", infer_eltypes=true)...) -panel = GigaSOM.DataFrame(GigaSOM.XLSX.readtable("PBMC8_panel.xlsx", "Sheet1", infer_eltypes=true)...) +import XLSX +md = GigaSOM.DataFrame(XLSX.readtable("PBMC8_metadata.xlsx", "Sheet1", infer_eltypes=true)...) +panel = GigaSOM.DataFrame(XLSX.readtable("PBMC8_panel.xlsx", "Sheet1", infer_eltypes=true)...) ``` After that, we can get the parameter structure from the first FCS files: From efdb5d2c23ca76407db063589f9758100f7ca1bf Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 7 Oct 2020 11:19:34 +0200 Subject: [PATCH 2/5] one extra forgotten fix --- docs/src/tutorials/processingFCSData.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/src/tutorials/processingFCSData.md b/docs/src/tutorials/processingFCSData.md index 775a472d..609e51a0 100644 --- a/docs/src/tutorials/processingFCSData.md +++ b/docs/src/tutorials/processingFCSData.md @@ -39,9 +39,12 @@ getMetaData(params) `data` is a matrix with cell expressions, one cell per row, one marker per column. If you want to run SOM analysis on it, you can cluster and visualize it -just as in the previous tutorial: +just as in the previous tutorial, with one exception- we start with cutting off +the `label` column that contains `NaN` values: ``` + +data = data[:,1:13] som = initGigaSOM(data, 16, 16) som = trainGigaSOM(som, data) clusters = mapToGigaSOM(som, data) From 6af9211b3afd2acc125485a8eaeb74442d3220ed Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 7 Oct 2020 11:20:15 +0200 Subject: [PATCH 3/5] convert XLSX import to a simpler `using` --- docs/src/tutorials/processingFCSData.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/src/tutorials/processingFCSData.md b/docs/src/tutorials/processingFCSData.md index 609e51a0..0f96f4bd 100644 --- a/docs/src/tutorials/processingFCSData.md +++ b/docs/src/tutorials/processingFCSData.md @@ -163,9 +163,9 @@ extract information about FCS data columns from there. First, we read the actual content using the XLSX package: ```julia -import XLSX -md = GigaSOM.DataFrame(XLSX.readtable("PBMC8_metadata.xlsx", "Sheet1", infer_eltypes=true)...) -panel = GigaSOM.DataFrame(XLSX.readtable("PBMC8_panel.xlsx", "Sheet1", infer_eltypes=true)...) +using XLSX +md = GigaSOM.DataFrame(readtable("PBMC8_metadata.xlsx", "Sheet1", infer_eltypes=true)...) +panel = GigaSOM.DataFrame(readtable("PBMC8_panel.xlsx", "Sheet1", infer_eltypes=true)...) ``` After that, we can get the parameter structure from the first FCS files: From a83fa33807ce7c358abfe07d2893f0502c8717a2 Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 7 Oct 2020 11:38:40 +0200 Subject: [PATCH 4/5] add RRID to the README Fixes #146 --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index c28d4983..18232f12 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,9 @@ GigaSOM is a Julia toolkit for clustering and visualisation of really large cytometry data. Most generally, it can load FCS files, perform transformation and cleaning operations in their contents, run FlowSOM-style clustering, and visualize and export the results. GigaSOM is distributed and parallel in nature, which makes processing huge datasets a breeze -- a hundred of millions of cells with a few dozen parameters can be clustered and visualized in a few minutes. -| **Documentation** | **Test Coverage** | **[ARTENOLIS](http://opencobra.github.io/artenolis)** | -|:-----------------:|:------------:|:--------------------------:| -| [![doc](https://img.shields.io/badge/doc-GigaSOM-blue)](http://git.io/GigaSOM.jl) | [![coverage status](http://codecov.io/github/LCSB-BioCore/GigaSOM.jl/coverage.svg?branch=master)](http://codecov.io/github/LCSB-BioCore/GigaSOM.jl?branch=master) | [![linux](https://prince.lcsb.uni.lu/jenkins/job/GigaSOM.jl-branches-auto-linux/badge/icon)](https://prince.lcsb.uni.lu/jenkins/job/GigaSOM.jl-branches-auto-linux/) | +| **Documentation** | **Test Coverage** | **[ARTENOLIS](http://opencobra.github.io/artenolis)** | **SciCrunch** | +|:-----------------:|:-----------------:|:-----------------------------------------------------:|:--------:| +| [![doc](https://img.shields.io/badge/doc-GigaSOM-blue)](http://git.io/GigaSOM.jl) | [![coverage status](http://codecov.io/github/LCSB-BioCore/GigaSOM.jl/coverage.svg?branch=master)](http://codecov.io/github/LCSB-BioCore/GigaSOM.jl?branch=master) | [![linux](https://prince.lcsb.uni.lu/jenkins/job/GigaSOM.jl-branches-auto-linux/badge/icon)](https://prince.lcsb.uni.lu/jenkins/job/GigaSOM.jl-branches-auto-linux/) | [![rrid](https://img.shields.io/badge/RRID-SCR__019020-72c02c)](https://scicrunch.org/resolver/RRID:SCR_019020) | # How to get started From a4116b3c154e719eb87bd9083c5a4c669264487d Mon Sep 17 00:00:00 2001 From: laurentheirendt Date: Wed, 7 Oct 2020 13:34:06 +0200 Subject: [PATCH 5/5] bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 45069e93..707013f7 100644 --- a/Project.toml +++ b/Project.toml @@ -1,6 +1,6 @@ name = "GigaSOM" uuid = "a03a9c34-069e-5582-a11c-5c984cab887c" -version = "0.6.0" +version = "0.6.1" [deps] CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"