Add many more figures in chapter 2

.gitignore

@@ -10,5 +10,8 @@
 # Data doesn't go in git
 /data
 
+# LyX backup file
+*.emergency
+
 # Snakemake temp files
 /.snakemake

Snakefile

@@ -215,6 +215,11 @@ rule png_crop:
     output: pdf = 'graphics/{basename}-CROP.png'
     shell: 'magick {input:q} -trim {output:q}'
 
+rule svg_to_pdf:
+    input: 'graphics/{filename}.svg'
+    output: 'graphics/{filename}-SVG.pdf'
+    shell: '''inkscape {input:q} --export-pdf={output:q} --export-dpi=300'''
+
 rule R_to_html:
     '''Render an R script as syntax-hilighted HTML.'''
     input: '{dirname}/{basename,[^/]+}.R'

thesis.lyx

@@ -698,7 +698,15 @@ Completely reimplement analysis from scratch as a reproducible workflow
 
 \begin_layout Itemize
 Use newly published methods & algorithms not available during the original
- analysis: SICER, csaw, MOFA, ComBat, sva, GREAT, and more
+ analysis: SICER, csaw, MOFA 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "Argelaguet2018"
+literal "false"
+
+\end_inset
+
+, ComBat, sva, GREAT, and more
 \end_layout
 
 \end_deeper
@@ -728,6 +736,20 @@ Focus on what hypotheses were tested, then select figures that show how
 \end_inset
 
 
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Maybe reorder these sections to do RNA-seq, then ChIP-seq, then combined
+ analyses?
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Subsection
@@ -1184,6 +1206,7 @@ status open
 \align center
 \begin_inset Graphics
 	filename graphics/CD4-csaw/Promoter Peak Distance Profile-PAGE1-CROP.pdf
+	lyxscale 50
 	width 100col%
 	groupId colwidth
 
@@ -1467,12 +1490,783 @@ status collapsed
 
 \end_layout
 
-\begin_layout Plain Layout
-\begin_inset Caption Standard
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+Comparison of quantification between Salmon with and without Shoal for identical
+ annotation
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+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.
+ To note in discussion: reproducible workflow made it easy to do this, enabling
+ an informed decision.
+\end_layout
+
+\begin_layout Subsection
+RNA-seq has a large confounding batch effect
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/RNA-seq/weights-vs-covars-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:RNA-seq-weights-vs-covars"
+
+\end_inset
+
+RNA-seq sample weights, grouped by experimental and technical covariates
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+
+\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/RNA-seq/PCA-no-batchsub-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:RNA-PCA-no-batchsub"
+
+\end_inset
+
+RNA-seq PCoA plot showing clear batch effect
+\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/RNA-seq/PCA-naive-batchsub-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:RNA-PCA-limma-batchsub"
+
+\end_inset
+
+RNA-seq PCoA plot showing clear batch effect
+\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/RNA-seq/PCA-combat-batchsub-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:RNA-PCA-ComBat-batchsub"
+
+\end_inset
+
+RNA-seq PCoA plot showing clear batch effect
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+RNA-seq batch effect can be partially corrected, but still induces uncorrectable
+ biases in downstream analysis
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Figures showing p-value histograms for within-batch and cross-batch contrasts,
+ showing that cross-batch contrasts have attenuated signal, as do comparisons
+ within the bad batch
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+ChIP-seq blacklisting is important
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/csaw/CCF-plots-PAGE2-CROP.pdf
+	lyxscale 50
+	width 100col%
+	groupId colwidth
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+Cross-correlation plots with blacklisted reads removed
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/csaw/CCF-plots-noBL-PAGE2-CROP.pdf
+	lyxscale 50
+	width 100col%
+	groupId colwidth
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+Cross-correlation plots without removing blacklisted reads
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Un-break the figure legend
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/csaw/CCF-max-plot-CROP.pdf
+	lyxscale 50
+	width 100col%
+	groupId colwidth
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+Estimated fragment size in samples before and after blacklisting
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+ChIP-seq normalization
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me2-sample-MAplot-bins-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
+MA plot of H3K4me2 read counts in 10kb bins for two arbitrary samples
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me3-sample-MAplot-bins-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
+MA plot of H3K4me3 read counts in 10kb bins for two arbitrary samples
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K27me3-sample-MAplot-bins-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
+MA plot of H3K27me3 read counts in 10kb bins for two arbitrary samples
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+ChIP-seq must be corrected for hidden confounding factors
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me2-PCA-raw-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:PCoA-H3K4me2-bad"
+
+\end_inset
+
+PCoA plot of H3K4me2 windows, before subtracting surrogate variables
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me2-PCA-SVsub-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:PCoA-H3K4me2-good"
+
+\end_inset
+
+PCoA plot of H3K4me2 windows, after subtracting surrogate variables
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me3-PCA-raw-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:PCoA-H3K4me3-bad"
+
+\end_inset
+
+PCoA plot of H3K4me3 windows, before subtracting surrogate variables
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me3-PCA-SVsub-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:PCoA-H3K4me3-good"
+
+\end_inset
+
+PCoA plot of H3K4me3 windows, after subtracting surrogate variables
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K27me3-PCA-raw-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:PCoA-H3K27me3-bad"
+
+\end_inset
+
+PCoA plot of H3K27me3 windows, before subtracting surrogate variables
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K27me3-PCA-SVsub-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:PCoA-H3K27me3-good"
+
+\end_inset
+
+PCoA plot of H3K27me3 windows, after subtracting surrogate variables
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+Figures showing BCV plots with and without SVA for each histone mark.
+\end_layout
+
+\begin_layout Itemize
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Can I do supplementary data on a thesis? This is a lot of plots for this
+ section.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+H3K4 and H3K27 promoter methylation has broadly the expected correlation
+ with gene expression
+\end_layout
+
+\begin_layout Itemize
+H3K4 is correlated with higher expression, and H3K27 is correlated with
+ lower expression genome-wide
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex TODO Note (inline)
+status open
 
 \begin_layout Plain Layout
-Comparison of quantification between Salmon with and without Shoal for identical
- annotation
+Grr, gotta find these figures.
+ Maybe in the old analysis?
 \end_layout
 
 \end_inset
@@ -1480,33 +2274,31 @@ Comparison of quantification between Salmon with and without Shoal for identical
 
 \end_layout
 
-\end_inset
-
-
+\begin_layout Itemize
+Figures showing these correlations: box/violin plots of expression distributions
+ with every combination of peak presence/absence in promoter
 \end_layout
 
 \begin_layout Itemize
-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.
- To note in discussion: reproducible workflow made it easy to do this, enabling
- an informed decision.
+Appropriate statistical tests showing significant differences in expected
+ directions
 \end_layout
 
 \begin_layout Subsection
-RNA-seq has a large confounding batch effect
+MOFA recovers biologically relevant variation from blind analysis by correlating
+ across datasets
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float figure
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename graphics/CD4-csaw/RNA-seq/weights-vs-covars-CROP.png
+	filename graphics/CD4-csaw/MOFA-varExplaiend-matrix-CROP.png
 	lyxscale 25
 	width 100col%
 	groupId colwidth-raster
@@ -1524,11 +2316,11 @@ status open
 \series bold
 \begin_inset CommandInset label
 LatexCommand label
-name "fig:RNA-seq-weights-vs-covars"
+name "fig:mofa-varexplained"
 
 \end_inset
 
-RNA-seq sample weights, grouped by experimental and technical covariates
+Variance explained in each data set by each latent factor estimated by MOFA.
 \end_layout
 
 \end_inset
@@ -1536,25 +2328,35 @@ RNA-seq sample weights, grouped by experimental and technical covariates
 
 \end_layout
 
-\begin_layout Plain Layout
+\end_inset
+
 
 \end_layout
 
-\end_inset
+\begin_layout Itemize
+Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:mofa-varexplained"
+plural "false"
+caps "false"
+noprefix "false"
 
+\end_inset
 
+ shows that LF1, 4, and 5 explain substantial var in all data sets
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float figure
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename graphics/CD4-csaw/RNA-seq/PCA-no-batchsub-CROP.png
+	filename graphics/CD4-csaw/MOFA-LF-distributions-CROP.png
 	lyxscale 25
 	width 100col%
 	groupId colwidth-raster
@@ -1572,11 +2374,11 @@ status open
 \series bold
 \begin_inset CommandInset label
 LatexCommand label
-name "fig:RNA-PCA-no-batchsub"
+name "fig:mofa-lf-dist"
 
 \end_inset
 
-RNA-seq PCoA plot showing clear batch effect
+Sample distribution for each latent factor estimated by MOFA.
 \end_layout
 
 \end_inset
@@ -1593,12 +2395,12 @@ RNA-seq PCoA plot showing clear batch effect
 \begin_inset Float figure
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename graphics/CD4-csaw/RNA-seq/PCA-naive-batchsub-CROP.png
+	filename graphics/CD4-csaw/MOFA-LF-scatter-CROP.png
 	lyxscale 25
 	width 100col%
 	groupId colwidth-raster
@@ -1616,11 +2418,16 @@ status open
 \series bold
 \begin_inset CommandInset label
 LatexCommand label
-name "fig:RNA-PCA-no-batchsub-1"
+name "fig:mofa-lf-scatter"
 
 \end_inset
 
-RNA-seq PCoA plot showing clear batch effect
+Scatter plots of specific pairs of MOFA latent factors.
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \end_inset
@@ -1628,21 +2435,45 @@ RNA-seq PCoA plot showing clear batch effect
 
 \end_layout
 
+\begin_layout Itemize
+Figures 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:mofa-lf-dist"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+ and 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:mofa-lf-scatter"
+plural "false"
+caps "false"
+noprefix "false"
+
 \end_inset
 
+ show that those same 3 LFs, (1, 4, & 5) also correlate best with the experiment
+al factors (cell type & time point)
+\end_layout
 
+\begin_layout Itemize
+LF2 is clearly the RNA-seq batch effect
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float figure
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename graphics/CD4-csaw/RNA-seq/PCA-combat-batchsub-CROP.png
+	filename graphics/CD4-csaw/MOFA-batch-correct-CROP.png
 	lyxscale 25
 	width 100col%
 	groupId colwidth-raster
@@ -1660,11 +2491,11 @@ status open
 \series bold
 \begin_inset CommandInset label
 LatexCommand label
-name "fig:RNA-PCA-no-batchsub-2"
+name "fig:mofa-batchsub"
 
 \end_inset
 
-RNA-seq PCoA plot showing clear batch effect
+Result of RNA-seq batch-correction using MOFA latent factors
 \end_layout
 
 \end_inset
@@ -1678,120 +2509,120 @@ RNA-seq PCoA plot showing clear batch effect
 \end_layout
 
 \begin_layout Itemize
-RNA-seq batch effect can be partially corrected, but still induces uncorrectable
- biases in downstream analysis
-\end_layout
+Attempting to remove the effect of LF2 (Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:mofa-batchsub"
+plural "false"
+caps "false"
+noprefix "false"
 
-\begin_deeper
-\begin_layout Itemize
-Figure showing MDS plot before & after ComBat
-\end_layout
+\end_inset
 
-\begin_layout Itemize
-Figure relating sample weights to batches, cell types, time points, etc.,
- showing that one batch is significantly worse quality
-\end_layout
+) results in batch correction comparable to ComBat (Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:RNA-PCA-ComBat-batchsub"
+plural "false"
+caps "false"
+noprefix "false"
 
-\begin_layout Itemize
-Figures showing p-value histograms for within-batch and cross-batch contrasts,
- showing that cross-batch contrasts have attenuated signal, as do comparisons
- within the bad batch
-\end_layout
+\end_inset
 
-\end_deeper
-\begin_layout Subsection
-ChIP-seq must be corrected for hidden confounding factors
+)
 \end_layout
 
 \begin_layout Itemize
-Figures showing pre- and post-SVA MDS plots for each histone mark
+MOFA was able to do this batch subtraction without directly using the sample
+ labels (sample labels were used implicitly to select which factor to subtract)
 \end_layout
 
 \begin_layout Itemize
-Figures showing BCV plots with and without SVA for each histone mark
+Similarity of results shows that batch correction can't get much better
+ than ComBat (despite ComBat ignoring time point)
 \end_layout
 
 \begin_layout Subsection
-H3K4 and H3K27 promoter methylation has broadly the expected correlation
- with gene expression
+Naive-to-memory convergence observed in H3K4 and RNA-seq data, not in H3K27me3
 \end_layout
 
-\begin_layout Itemize
-H3K4 is correlated with higher expression, and H3K27 is correlated with
- lower expression genome-wide
-\end_layout
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
 
-\begin_layout Itemize
-Figures showing these correlations: box/violin plots of expression distributions
- with every combination of peak presence/absence in promoter
-\end_layout
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/RNA-seq/PCA-final-23-CROP.png
+	lyxscale 25
+	width 100col%
+	groupId colwidth-raster
+
+\end_inset
 
-\begin_layout Itemize
-Appropriate statistical tests showing significant differences in expected
- directions
-\end_layout
 
-\begin_layout Subsection
-MOFA recovers biologically relevant variation from blind analysis by correlating
- across datasets
 \end_layout
 
-\begin_layout Itemize
-MOFA 
-\begin_inset CommandInset citation
-LatexCommand cite
-key "Argelaguet2018"
-literal "false"
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:RNA-PCA-group"
 
 \end_inset
 
- successfully separates biologically relevant patterns of variation from
- technical confounding factors without knowing the sample labels, by finding
- latent factors that explain variation across multiple data sets.
+RNA-seq PCoA showing principal coordiantes 2 and 3.
 \end_layout
 
-\begin_deeper
-\begin_layout Itemize
-Figure: show percent-variance-explained plot from MOFA and PCA-like plots
- for the relevant latent factors
-\end_layout
+\end_inset
+
 
-\begin_layout Itemize
-MOFA analysis also shows that batch effect correction can't get much better
- than it already is (Figure comparing blind MOFA batch correction to ComBat
- correction)
 \end_layout
 
-\end_deeper
-\begin_layout Subsection
-Naive-to-memory convergence observed in H3K4 and RNA-seq data, not in H3K27me3
+\end_inset
+
+
 \end_layout
 
 \begin_layout Itemize
 H3K4 and RNA-seq data show clear evidence of naive convergence with memory
- between days 1 and 5 (MDS plot figure, also compare with last figure from
- 
-\begin_inset CommandInset citation
-LatexCommand cite
-key "LaMere2016"
-literal "false"
+ between days 1 and 5 (Figures 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:PCoA-H3K4me2-good"
+plural "false"
+caps "false"
+noprefix "false"
 
 \end_inset
 
-)
-\end_layout
+, 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:PCoA-H3K4me3-good"
+plural "false"
+caps "false"
+noprefix "false"
 
-\begin_layout Standard
-\begin_inset Flex TODO Note (inline)
-status open
+\end_inset
 
-\begin_layout Plain Layout
-Note that Sarah has granted permission to use her figures
-\end_layout
+, and 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:RNA-PCA-group"
+plural "false"
+caps "false"
+noprefix "false"
 
 \end_inset
 
-
+.
 \end_layout
 
 \begin_layout Itemize
@@ -1800,7 +2631,17 @@ Table of numbers of genes different between N & M at each time point, showing
 \end_layout
 
 \begin_layout Itemize
-Similar figure for H3K27me3 showing lack of convergence
+Similar figure for H3K27me3 showing lack of convergence (Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:PCoA-H3K27me3-good"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+)
 \end_layout
 
 \begin_layout Subsection
@@ -1841,6 +2682,12 @@ MOFA shows great promise for accelerating discovery of major biological
 \end_layout
 
 \begin_deeper
+\begin_layout Itemize
+MOFA successfully separates biologically relevant patterns of variation
+ from technical confounding factors without knowing the sample labels, by
+ finding latent factors that explain variation across multiple data sets.
+\end_layout
+
 \begin_layout Itemize
 MOFA was added to this analysis late and played primarily a confirmatory
  role, but it was able to confirm earlier conclusions with much less prior
@@ -1860,9 +2707,59 @@ Naive-to-memory convergence implies that naive cells are differentiating
  in this differentiation while H3K27me3 is less involved
 \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/LaMere2016_fig8.pdf
+	lyxscale 50
+	width 100col%
+	groupId colwidth
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+LaMere 2016 Figure 8, reproduced with permission.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+Convergence is consistent with Lamere2016 fig 8 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "LaMere2016"
+literal "false"
+
+\end_inset
+
+ (which was created without the benefit of SVA)
+\end_layout
+
 \begin_layout Itemize
 H3K27me3, canonically regarded as a deactivating mark, seems to have a more
- complex
+ complex effect
 \end_layout
 
 \begin_layout Itemize
@@ -2894,6 +3791,7 @@ status collapsed
 \align center
 \begin_inset Graphics
 	filename graphics/PAM/predplot.pdf
+	lyxscale 50
 	width 100col%
 	groupId colwidth
 
@@ -2974,6 +3872,7 @@ status collapsed
 \align center
 \begin_inset Graphics
 	filename graphics/PAM/ROC-TXvsAR-internal.pdf
+	lyxscale 50
 	width 100col%
 	groupId colwidth
 
@@ -3632,6 +4531,7 @@ status collapsed
 \align center
 \begin_inset Graphics
 	filename graphics/PAM/ROC-TXvsAR-external.pdf
+	lyxscale 50
 	width 100col%
 	groupId colwidth