Add Promoter neighborhood plots

thesis.lyx

@@ -558,6 +558,7 @@ status open
 \align center
 \begin_inset Graphics
 	filename graphics/CD4-csaw/rulegraphs/rulegraph-all.pdf
+	lyxscale 50
 	width 100theight%
 
 \end_inset
@@ -1512,6 +1513,7 @@ Comparison of quantification between Salmon with and without Shoal for identical
 Ultimately selected shoal as quantification, Ensembl as annotation.
  Why? Running downstream analyses with all quant methods and both annotations
  showed very little practical difference, so choice was not terribly important.
+ Prefer shoal due to theoretical advantages.
  To note in discussion: reproducible workflow made it easy to do this, enabling
  an informed decision.
 \end_layout
@@ -2648,6 +2650,270 @@ noprefix "false"
 Effect of promoter coverage upstream vs downstream of TSS
 \end_layout
 
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-clusters-CROP.png
+	lyxscale 25
+	width 100col%
+	groupId colwidth-raster
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:H3K4me2-neighborhood-clusters"
+
+\end_inset
+
+RNA-seq PCoA showing principal coordiantes 2 and 3.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-PCA-CROP.png
+	lyxscale 25
+	width 100col%
+	groupId colwidth-raster
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:H3K4me2-neighborhood-pca"
+
+\end_inset
+
+RNA-seq PCoA showing principal coordiantes 2 and 3.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-expression-CROP.png
+	lyxscale 25
+	width 100col%
+	groupId colwidth-raster
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:H3K4me2-neighborhood-expression"
+
+\end_inset
+
+RNA-seq PCoA showing principal coordiantes 2 and 3.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-clusters-CROP.png
+	lyxscale 25
+	width 100col%
+	groupId colwidth-raster
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:H3K4me3-neighborhood-clusters"
+
+\end_inset
+
+RNA-seq PCoA showing principal coordiantes 2 and 3.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-PCA-CROP.png
+	lyxscale 25
+	width 100col%
+	groupId colwidth-raster
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:H3K4me3-neighborhood-pca-1"
+
+\end_inset
+
+RNA-seq PCoA showing principal coordiantes 2 and 3.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-expression-CROP.png
+	lyxscale 25
+	width 100col%
+	groupId colwidth-raster
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:H3K4me3-neighborhood-expression-1"
+
+\end_inset
+
+RNA-seq PCoA showing principal coordiantes 2 and 3.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Itemize
 H3K4me peaks seem to correlate with increased expression as long as they
  are anywhere near the TSS