Fix images layout and delete obsolete ones

Author: stephan-koenig

golden_data.Rmd

@@ -24,15 +24,15 @@ To show you how to access these data, we will download the alpha subunit sequenc
 
 First, navigate to <http://fungene.cme.msu.edu/>. This front page organizes the genes into their respective functional groups. The sequences we're interested in are involved in biogeochemical cycling, so look under that panel for "AmoA" and "PmoA".
 
-![](images/fungene_landing.png)
+![](images/fungene_landing.png){width=50%}
 
 As you can see, AmoA are broken up into four different entries: "amoA_AOA", "amoA_AOB", "amoA_AOB_like", and "amoA_comammox". We will download the sequences from only "amoA_AOA" and "amoA_AOB", so let's begin alphabetically with "amoA_AOA".
 
-![](images/amoA_AOA_landing.png)
+![](images/amoA_AOA_landing.png){width=50%}
 
 For these sequences, we will limit them to just sequences derived from isolate genomes of which the functional and taxonomic annotations are more reliable. To do this, go to "Display Options" in the top right. Click the "Isolate" option then "Update". We also want the sequences that are more-or-less full-length. Click on "Show/Hide filter options", fill the "Minimum HMM Coverage" parameter with "80" (or some other number between 60 and 90), then "Filter". That's all the filtering we're going to do here. To add the sequences to your cart, click "Select All Sequences" then "Begin Analysis".
 
-![](images/amoA_AOA_download.png)
+![](images/amoA_AOA_download.png){width=100%}
 
 Deselect "Aligned" then click the "Download" button.
 
@@ -42,7 +42,7 @@ Repeat with the above steps with the other genes "amoA_AOB" and "PmoA".
 
 Go to the EggNOG website at http://eggnog5.embl.de/#/app/home and search for either "ENOG5028JPK" or "arCOG08676" in the search bar at the top of the page. These EggNOG ortholog identifiers correspond to PmoA/AmoA from Bacteria and AmoA from Archaea, respectively. In the image below, we've searched for "ENOG5028JPK".
 
-![](images/EggNOG_xmoa_1.png)
+![](images/EggNOG_xmoa_1.png){width=100%}
 
 Click "Download" at the bottom-left of the panel and select "All _XX_ sequences (FASTA)", where _XX_ is the number of sequences belonging to the orthologous group (OG). This will open a new window with all sequences from that OG in FASTA format. Download this file to a file on your computer following the format &lt;OG name&gt;_EggNOGv5.faa where &lt;OG name&gt; is the EggNOG ortholog identifier.
 

images/XmoA_34_iTOL.png

@@ -16,7 +16,7 @@ Specifically, we will study the effects of changing oxygen levels on communities
 
 By combining multi-omics and geochemical parameter information from OMZs, it becomes possible to evaluate microbial communities' regulatory and response dynamics to changing DO levels. For example, because OMZs are hotspots for nitrogen loss processes reconstructing the nitrogen cycle as a distributed metabolic process can shed new insight into microbial controls on matter and energy transformations integral to ocean health and climate balance. Genes encoding key steps in the nitrogen cycle are well defined (Figure \@ref(fig:N-cycle-genes)), providing a basis for functional anchor screening to determine their distribution across the Tree of Life.
 
-```{r N-cycle-genes, echo = FALSE, fig.cap = "Nitrogen cycle"}
+```{r N-cycle-genes, echo = FALSE, fig.cap = "Nitrogen cycle", out.width = "100%"}
 knitr::include_graphics("images/N_cycle_genes.png")
 ```
 

images/XmoA_36_iTOL.png

@@ -249,7 +249,7 @@ scp -r root@<server address>:/data/ts_tutorial/p_amoA_FunGene9.5_isolates_update
 
 -   The two files `XmoA_Function_colours_style.txt` and `XmoA_Function_colour_strip.txt`  can be dragged into the iTOL browser window to bring colour to the XmoA tree. The figure should look identical to Figure \@ref(fig:XmoA-Classified)
 
-![(\#fig:XmoA-Classified)XmoA phylogeny after functional annotation](images/XmoA_update_coloured.png )
+![(\#fig:XmoA-Classified)XmoA phylogeny after functional annotation](images/XmoA_update_coloured.png){width=100%}
 
 -   Finally, turn on the "Phylogenetic Placements" dataset (right of the screen).
 

images/XmoA_classified.png

@@ -147,7 +147,7 @@ The `treesapp assign` output directory (defined by the flag `--output`, i.e. in
 
 -   Finally, turn on the "Phylogenetic Placements" dataset (right of the screen) and the figure should look identical to this figure below Figure \@ref(fig:xmoa).
 
-    ![(\#fig:xmoa) Phylogenetic tree of XmoA_seed refpkg. The red bubbles represent sequence placements with the size of the bubble indicating the number of placements on a branch. 76 sequences were classified and placed on 36 leaf nodes. ](images/XmoA_seed_iTOLtree.svg)
+    ![(\#fig:xmoa) Phylogenetic tree of XmoA_seed refpkg. The red bubbles represent sequence placements with the size of the bubble indicating the number of placements on a branch. 76 sequences were classified and placed on 36 leaf nodes. ](images/XmoA_seed_iTOLtree.svg){width=100%}
 
 ## Building your group's reference package