diff --git a/deicode/q2/tests/test_method.py b/deicode/q2/tests/test_method.py index 4bba31e..925f475 100644 --- a/deicode/q2/tests/test_method.py +++ b/deicode/q2/tests/test_method.py @@ -58,10 +58,7 @@ def setUp(self): create_test_table()) def test_qiime2_rpca(self): - """Tests that the Q2 and standalone RPCA results match. - - Also validates against ground truth "expected" results. - """ + """Tests that the Q2 and standalone RPCA results match.""" tstdir = "test_output" # Run DEICODE through QIIME 2 (specifically, the Artifact API) diff --git a/ipynb/tutorials/etc/img10.png b/ipynb/tutorials/etc/img10.png new file mode 100644 index 0000000..0b9e2ae Binary files /dev/null and b/ipynb/tutorials/etc/img10.png differ diff --git a/ipynb/tutorials/etc/img11.png b/ipynb/tutorials/etc/img11.png new file mode 100644 index 0000000..1962267 Binary files /dev/null and b/ipynb/tutorials/etc/img11.png differ diff --git a/ipynb/tutorials/moving-pictures.ipynb b/ipynb/tutorials/moving-pictures.ipynb index b142150..51d348e 100644 --- a/ipynb/tutorials/moving-pictures.ipynb +++ b/ipynb/tutorials/moving-pictures.ipynb @@ -161,7 +161,7 @@ "source": [ "Biplots are exploratory visualization tools that allow us to represent the features (i.e. taxonomy or OTUs) that strongly influence the principal component axis as arrows. The interpretation of the compositional biplot differs slightly from classical biplot interpretation (we can view the qzv file at [view.qiime2](https://view.qiime2.org). The important features with regard to sample clusters are not a single arrow but by the log ratio between features represented by arrows pointing in different directions. A visualization tool for these log ratios is coming soon to QIIME. \n", "\n", - "![](etc/img8.png)\n", + "![](etc/img10.png)\n", "\n", "From this visualization we noticed that BodySite seems to explain the clusters well. We can run [PERMANOVA](https://docs.qiime2.org/2019.1/plugins/available/diversity/beta-group-significance/) on the distances to get a statistical significance for this. " ] @@ -194,15 +194,8 @@ "source": [ "Indeed we can now see that the clusters we saw in the biplot were significant by viewing the BodySite_significance.qzv at [view.qiime2](https://view.qiime2.org).\n", "\n", - "![](etc/img9.png)" + "![](etc/img11.png)" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -221,7 +214,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.5" + "version": "3.6.7" } }, "nbformat": 4, diff --git a/ipynb/tutorials/moving-pictures.md b/ipynb/tutorials/moving-pictures.md index 0d4578c..f3c8c46 100644 --- a/ipynb/tutorials/moving-pictures.md +++ b/ipynb/tutorials/moving-pictures.md @@ -116,7 +116,7 @@ qiime emperor biplot \ Biplots are exploratory visualization tools that allow us to represent the features (i.e. taxonomy or OTUs) that strongly influence the principal component axis as arrows. The interpretation of the compositional biplot differs slightly from classical biplot interpretation (we can view the qzv file at [view.qiime2](https://view.qiime2.org). The important features with regard to sample clusters are not a single arrow but by the log ratio between features represented by arrows pointing in different directions. A visualization tool for these log ratios is coming soon to QIIME. -![](etc/img8.png) +![](etc/img10.png) From this visualization we noticed that BodySite seems to explain the clusters well. We can run [PERMANOVA](https://docs.qiime2.org/2019.1/plugins/available/diversity/beta-group-significance/) on the distances to get a statistical significance for this. @@ -131,7 +131,7 @@ From this visualization we noticed that BodySite seems to explain the clusters w Indeed we can now see that the clusters we saw in the biplot were significant by viewing the BodySite_significance.qzv at [view.qiime2](https://view.qiime2.org). -![](etc/img9.png) +![](etc/img11.png) ## Citation diff --git a/ipynb/tutorials/qiime2-moving-pictures-tutorial/BodySite_significance.qzv b/ipynb/tutorials/qiime2-moving-pictures-tutorial/BodySite_significance.qzv index 900b020..08e519a 100644 Binary files a/ipynb/tutorials/qiime2-moving-pictures-tutorial/BodySite_significance.qzv and b/ipynb/tutorials/qiime2-moving-pictures-tutorial/BodySite_significance.qzv differ diff --git a/ipynb/tutorials/qiime2-moving-pictures-tutorial/biplot.qzv b/ipynb/tutorials/qiime2-moving-pictures-tutorial/biplot.qzv index f304e09..32038e9 100644 Binary files a/ipynb/tutorials/qiime2-moving-pictures-tutorial/biplot.qzv and b/ipynb/tutorials/qiime2-moving-pictures-tutorial/biplot.qzv differ diff --git a/ipynb/tutorials/qiime2-moving-pictures-tutorial/distance.qza b/ipynb/tutorials/qiime2-moving-pictures-tutorial/distance.qza index 1e442e7..db33769 100644 Binary files a/ipynb/tutorials/qiime2-moving-pictures-tutorial/distance.qza and b/ipynb/tutorials/qiime2-moving-pictures-tutorial/distance.qza differ diff --git a/ipynb/tutorials/qiime2-moving-pictures-tutorial/ordination.qza b/ipynb/tutorials/qiime2-moving-pictures-tutorial/ordination.qza index d135b8f..ac86be5 100644 Binary files a/ipynb/tutorials/qiime2-moving-pictures-tutorial/ordination.qza and b/ipynb/tutorials/qiime2-moving-pictures-tutorial/ordination.qza differ