From 4a0944805b5b980a0abf43e7dd0c797fd0fb3447 Mon Sep 17 00:00:00 2001
From: johnne <john.sundh@scilifelab.se>
Date: Thu, 28 Apr 2022 10:30:32 +0200
Subject: [PATCH 1/3] Update jupyter code in extra material

---
 pages/jupyter/jupyter-9-extra-material.md | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/pages/jupyter/jupyter-9-extra-material.md b/pages/jupyter/jupyter-9-extra-material.md
index ed5630ab..c78ef2b4 100644
--- a/pages/jupyter/jupyter-9-extra-material.md
+++ b/pages/jupyter/jupyter-9-extra-material.md
@@ -86,6 +86,7 @@ find an example in the code chunk below:
 rule make_supplementary:
     input:
         counts = "results/tables/counts.tsv",
+        summary = "results/tables/counts.tsv.summary",
         multiqc_file = "intermediate/multiqc_general_stats.txt",
         rulegraph = "results/rulegraph.png"
     output:
@@ -151,6 +152,7 @@ version of the notebook using the `log: notebook=` directive:
 rule make_supplementary_plots:
     input:
         counts = "results/tables/counts.tsv",
+        summary = "results/tables/counts.tsv.summary",
         multiqc = "intermediate/multiqc_general_stats.txt",
         rulegraph = "results/rulegraph.png"
     output:
@@ -167,6 +169,7 @@ defined notebook parameters edit the code so that it looks like this:
 
 ```python
 counts_file=snakemake.input.counts
+summary_file=snakemake.input.summary
 multiqc_file=snakemake.input.multiqc
 rulegraph_file=snakemake.input.rulegraph
 
@@ -209,25 +212,23 @@ to save the plots to the output files. First, edit the cell that generates the
 barplot so that it looks like this:
 
 ```python
-count_data = pd.DataFrame(counts.sum(), columns = ["genes"])
-count_data = pd.merge(count_data, counts_other.T, left_index=True, right_index=True)
-
-colors = sns.color_palette("husl", n_colors=count_data.shape[1])
-ax = count_data.plot(kind="bar", stacked=True, color=colors)
-ax.legend(bbox_to_anchor=(1,1), title="Feature");
+# Create a stacked barplot
+ax = summary_plot_data.T.plot(kind="bar", stacked=True, color=colors)
+# Move legend and set legend title
+ax.legend(bbox_to_anchor=(1,1), title="Category");
 plt.savefig(snakemake.output.barplot, dpi=300, bbox_inches="tight") ## <-- Add this line!
 ```
 
 Finally, edit the cell that generates the heatmap so that it looks like this:
 
 ```python
-heatmap_data = counts.loc[(counts.std(axis=1).div(counts.mean(axis=1))>1.2)&(counts.max(axis=1)>5)]
-heatmap_data = heatmap_data.rename(index=lambda x: f"{x} ({gene_names[x]})")
-heatmap_data.rename(columns = lambda x: name_dict['title'][x], inplace=True)
+count_data = counts.loc[:, SRR_IDs]
+heatmap_data = count_data.loc[(count_data.std(axis=1).div(count_data.mean(axis=1))>1.2)&(count_data.max(axis=1)>5)]
+heatmap_data = heatmap_data.rename(columns = name_dict['title'])
 with sns.plotting_context("notebook", font_scale=0.7):
     ax = sns.clustermap(data=np.log10(heatmap_data+1), cmap="RdYlBu_r", 
                         method="complete", yticklabels=True, linewidth=.5,
-                        cbar_pos=(0.2, .8, 0.02, 0.15), figsize=(8,6))
+                        cbar_pos=(.7, .85, .05, .1), figsize=(3,9))
     plt.setp(ax.ax_heatmap.get_xticklabels(), rotation=270)
     plt.savefig(snakemake.output.heatmap, dpi=300, bbox_inches="tight") ## <-- Add this line!
 ```

From 31f3f7ddbc72331554b6f9bd856e49bf6f5db8ca Mon Sep 17 00:00:00 2001
From: johnne <john.sundh@scilifelab.se>
Date: Thu, 28 Apr 2022 10:31:49 +0200
Subject: [PATCH 2/3] Update nbconvert version due to error

---
 tutorials/jupyter/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/jupyter/environment.yml b/tutorials/jupyter/environment.yml
index 0a8875f1..78c121e0 100644
--- a/tutorials/jupyter/environment.yml
+++ b/tutorials/jupyter/environment.yml
@@ -11,6 +11,6 @@ dependencies:
   - seaborn=0.11.2
   - matplotlib=3.5.0
   - ipywidgets=7.6.5
-  - nbconvert=5.6.1
+  - nbconvert=6.5.0
   - jinja2<=3.0.3
   - jupyter_contrib_nbextensions=0.5.1
\ No newline at end of file

From 37b62068ac75188ab8dd95944fd7e5302a59ada8 Mon Sep 17 00:00:00 2001
From: johnne <john.sundh@scilifelab.se>
Date: Thu, 28 Apr 2022 10:58:37 +0200
Subject: [PATCH 3/3] Downgrade nbconvert again

---
 tutorials/jupyter/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/jupyter/environment.yml b/tutorials/jupyter/environment.yml
index 78c121e0..0a8875f1 100644
--- a/tutorials/jupyter/environment.yml
+++ b/tutorials/jupyter/environment.yml
@@ -11,6 +11,6 @@ dependencies:
   - seaborn=0.11.2
   - matplotlib=3.5.0
   - ipywidgets=7.6.5
-  - nbconvert=6.5.0
+  - nbconvert=5.6.1
   - jinja2<=3.0.3
   - jupyter_contrib_nbextensions=0.5.1
\ No newline at end of file