Shrink figures

Author: zamiqbal

_posts/2015-12-17-Test-Driving-Nanopore-Assemblies.md

@@ -60,15 +60,13 @@ The first thing to note is that both the LQS and Phillippy group assembly pipeli
 
 
 Looking at the mummerplots, we can see that all three assemblies align nicely to the reference. Here is the LQS assembly:
-![][fig1]
+<img src="{{site.baseurl}}/assets/img/20151215_poligraph_Ecoli_K12_loman_and_nanopolish.mdelta.png" height="50%" width="50%">
+
 and here the PBcR assembly
-![some text][fig2]
+<img src="{{site.baseurl}}/assets/img/20151215_poligraph_Ecoli_K12_PBcR_and_2nd_nanopolish.mdelta.png" height="50%" width="50%">
 and finally the Miniasm assembly:
-![some text][fig3]
+<img src="{{site.baseurl}}/assets/img/20151215_poligraph_Ecoli_K12_miniasm.mdelta.png" height="50%" width="50%">
 
-[fig1]: {{site.baseurl}}/assets/img/20151215_poligraph_Ecoli_K12_loman_and_nanopolish.mdelta.png
-[fig2]: {{site.baseurl}}/assets/img/20151215_poligraph_Ecoli_K12_PBcR_and_2nd_nanopolish.mdelta.png
-[fig3]: {{site.baseurl}}/assets/img/20151215_poligraph_Ecoli_K12_miniasm.mdelta.png
 
 Once we allow for the fact that they will each have linearised the circular chromosome in different places, we see that all are consistent with the truth assembly.
 
@@ -120,24 +118,15 @@ Tables of results and mummer plots
 Unlike the K12 Loman dataset, here all the assemblers fail to produce a single-contig assembly. However, all of the assemblies were consistent and agreed structurally with the truth, apart from one putative inversion ?kb long. This could be due to evolution since the origina assembly was performed, we would have to check. 
 
 For PBcR
-
-![some text][fig4]
-
-[fig4]: {{site.baseurl}}/assets/img/JR_FAA63658_29092015_ecol_P46212_PBcR_nano_poli_vs_mini_nano_poli.mdelta.png
+<img src="{{site.baseurl}}/assets/img/JR_FAA63658_29092015_ecol_P46212_PBcR_nano_poli_vs_mini_nano_poli.mdelta.png" height="50%" width="50%">
 
 and for miniasm
-
-![some text][fig5]
-
-[fig5]: {{site.baseurl}}/assets/img/JR_FAA63658_29092015_ecol_P46212_miniasm_nano_poli.mdelta.png
+<img src="{{site.baseurl}}/assets/img/JR_FAA63658_29092015_ecol_P46212_miniasm_nano_poli.mdelta.png" height="50%" width="50%">
 
 
 These plots can be a little confusing (many thanks to Adam Phillippy for some patient emails helping us through some interpretation), but if we align the two assemblies against each other, we see that they are almost entirely consistent, supporting the possibility that the inversion we see with respect to the reference/truth is real.
 
-![some text][fig6]
-
-[fig6]: {{site.baseurl}}/assets/img/JR_FAA63658_29092015_ecol_P46212_PBcR_nano_poli_vs_mini_nano_poli.mdelta.png
-
+<img src="{{site.baseurl}}/assets/img/JR_FAA63658_29092015_ecol_P46212_PBcR_nano_poli_vs_mini_nano_poli.mdelta.png" height="50%" width="50%">
 
 
 
@@ -147,32 +136,21 @@ The second clinical sample was a K. pneumoniae clinical isolate with 4 plasmids.
 
 Table of results
 
-
+zahara <img src="" height="50%" width="50%">
 PBcR
-![some text][fig7]
-
-[fig7]: {{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_PBcR_nano_poli.mdelta.png
+<img src="{{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_PBcR_nano_poli.mdelta.png" height="50%" width="50%">
 
 and miniasm
-
-![some text][fig8]
-
-[fig8]: {{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_mini_poli.mdelta.png
+<img src="{{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_mini_poli.mdelta.png" height="50%" width="50%">
 
 If we zoom into look at the 4 plasmids in this sample, we see
 
 PBCr
-
-![some text][fig9]
-
-[fig9]: {{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_plasmid_PBcR_and_nanopolish_illumina_correction_plasmids.mdelta.png
+<img src="{{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_plasmid_PBcR_and_nanopolish_illumina_correction_plasmids.mdelta.png" height="50%" width="50%">
 
 
 and miniasm
-
-![some text][fig10]
-
-[fig10]: {{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_plasmid_miniasm_only_illumina_correction_plasmids.mdelta.png
+<img src="{{site.baseurl}}/assets/img/JR_FAA63668_14102015_kpne_CAV1596_plasmid_miniasm_only_illumina_correction_plasmids.mdelta.png" height="50%" width="50%">
 
 
 I guess we need to follow Adam's suggestion to check if PBcR can recover the plasmids. I assume this will work: