Mercurial > repos > iuc > scater_plot_pca

annotate README.md @ 2:bbfcd8c206ba draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:34:39 +0000
parents d6e5485b6e57
children 0472bd64cacf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
1 # Wrappers for Scater
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
2
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
3 This code wraps a number of [scater](https://bioconductor.org/packages/release/bioc/html/scater.html) functions as Galaxy wrappers. Briefly, the `scater-create-qcmetric-ready-sce` tool takes a sample gene expression matrix (usually read-counts) and a cell annotation file, creates a [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) object and runs scater's `calculateQCMetrics` function (using other supplied files such as ERCC's and mitochondrial gene features).
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
4 Various filter scripts are provided, along with some plotting functions for QC.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
5
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
6
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
7 ## Typical workflow
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
8
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
9 1. Read in data with `scater-create-qcmetric-ready-sce`.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
10 2. Visualise it.\
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
11 Take a look at the distribution of library sizes, expressed features and mitochondrial genes with `scater-plot-dist-scatter`.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
12 Then look at the distibution of genes across cells with `scater-plot-exprs-freq`.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
13 3. Guided by the plots, filter the data with `scater-filter`.\
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
14 You can either manually filter with user-defined parameters or use PCA to automatically removes outliers.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
15 4. Visualise data again to see how the filtering performed using `scater-plot-dist-scatter`.\
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
16 Decide if you're happy with the data. If not, try increasing or decreasing the filtering parameters.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
17 5. Normalise data with `scater-normalize`.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
18 6. Investigate other confounding factors.\
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
19 Plot the data (using PCA) and display various annotated properties of the cells using `scater-plot-pca`.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
20
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
21 ## Command-line usage
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
22
1
d6e5485b6e57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
23 The scripts require the installation of scater and few other R/BioConductor packages. An easy way to install them is to create a [conda](https://conda.io/) environment using the `environment.yml` file distributed together with these wrappers:
d6e5485b6e57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
24
d6e5485b6e57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
25 ```
d6e5485b6e57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
26 conda env create -f environment.yml
d6e5485b6e57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
27 conda activate scater
d6e5485b6e57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
28 ```
d6e5485b6e57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
29
0
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
30 For help with any of the following scripts, run:
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
31 `<script-name> --help`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
32
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
33 ---
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
34
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
35 `scater-create-qcmetric-ready-sce.R`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
36 Takes an expression matrix (usually read-counts) of samples (columns) and gene/transcript features (rows), along with other annotation information, such as cell metadata, control genes (mitochondrail genes, ERCC's), creates a [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) object and runs scater's `calculateQCMetrics`. Save the resulting SingleCellExperiment object in Loom format.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
37
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
38
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
39 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
40 ./scater-create-qcmetric-ready-sce.R -a test-data/counts.txt -c test-data/annotation.txt -f test-data/mt_controls.txt -o test-data/scater_qcready.loom
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
41 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
42
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
43 ---
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
44
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
45 `scater-plot-dist-scatter.R`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
46 Takes SingleCellExperiment object (from Loom file) and plots a panel of read and feature graphs, including the distribution of library sizes, distribution of feature counts, a scatterplot of reads vs features, and % of mitochondrial genes in library.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
47
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
48 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
49 ./scater-plot-dist-scatter.R -i test-data/scater_qcready.loom -o test-data/scater_reads_genes_dist.pdf
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
50 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
51
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
52 ---
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
53
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
54 `scater-plot-exprs-freq.R`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
55 Plots mean expression vs % of expressing cells and provides information as to the number of genes expressed in 50% and 25% of cells.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
56
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
57 ---
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
58
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
59 `scater-pca-filter.R`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
60 Takes SingleCellExperiment object (from Loom file) and automatically removes outliers from data using PCA. Save the filtered SingleCellExperiment object in Loom format.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
61
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
62 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
63 ./scater-pca-filter.R -i test-data/scater_qcready.loom -o test-data/scater_pca_filtered.loom
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
64 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
65
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
66 ---
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
67
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
68 `scater-manual-filter.R`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
69 Takes SingleCellExperiment object (from Loom file) and filters data using user-provided parameters. Save the filtered SingleCellExperiment object in Loom format.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
70
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
71 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
72 ./scater-manual-filter.R -i test-data/scater_qcready.loom -l 10000 -d 4 -m 33 -o test-data/scater_manual_filtered.loom
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
73 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
74
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
75 ---
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
76
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
77 `scater-normalize.R`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
78 Compute log-normalized expression values from count data in a SingleCellExperiment object, using the size factors stored in the object. Save the normalised SingleCellExperiment object in Loom format.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
79
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
80 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
81 ./scater-normalize.R -i test-data/scater_manual_filtered.loom -o test-data/scater_man_filtered_normalised.loom
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
82 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
83
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
84 ---
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
85
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
86 `scater-plot-pca.R`
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
87 PCA plot of a normalised SingleCellExperiment object (produced with `scater-normalize.R`). The options `-c`, `-p`, and `-s` all refer to cell annotation features. These are the column headers of the `-c` option used in `scater-create-qcmetric-ready-sce.R`.
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
88
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
89 ```
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
90 ./scater-plot-pca.R -i test-data/scater_man_filtered_normalised.loom -c Treatment -p Mutation_Status -o test-data/scater_pca_plot.pdf
fe0d9bb68ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
91 ```