Add a bunch of figures to chapter 2

.gitignore

@@ -5,6 +5,7 @@
 *RASTER.png
 *PAGE*.pdf
 *CROP.pdf
+*CROP.png
 
 # Data doesn't go in git
 /data

thesis.lyx

@@ -735,29 +735,758 @@ H3K4 and H3K27 methylation occur in broad regions and are enriched near
  promoters
 \end_layout
 
-\begin_layout Itemize
-Figures comparing MACS (non-broad peak caller) to SICER/epic (broad peak
- caller)
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Re-generate IDR rank consistency plots for SICER and MACS side-by-side
+\end_layout
+
+\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:IDR-RC-H3K4me2"
+
+\end_inset
+
+Irreproducible Discovery Rate consistency plots for H3K4me2
+\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
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Re-generate IDR rank consistency plots for SICER and MACS side-by-side
+\end_layout
+
+\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:IDR-RC-H3K4me3"
+
+\end_inset
+
+Irreproducible Discovery Rate consistency plots for H3K4me3
+\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
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Re-generate IDR rank consistency plots for SICER and MACS side-by-side
+\end_layout
+
+\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:IDR-RC-H3K27me3"
+
+\end_inset
+
+Irreproducible Discovery Rate consistency plots for H3K27me3
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float table
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Need 
+\emph on
+median
+\emph default
+ peak width, not mean
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Tabular
+<lyxtabular version="3" rows="4" columns="5">
+<features tabularvalignment="middle">
+<column alignment="center" valignment="top">
+<column alignment="center" valignment="top">
+<column alignment="center" valignment="top">
+<column alignment="center" valignment="top">
+<column alignment="center" valignment="top">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Histone Mark
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+# Peaks
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Mean peak width
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+genome coverage
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+read coverage
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+H3K4me2
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+14965
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+3970
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+1.92%
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+14.2%
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+H3K4me3
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+6163
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+2946
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+0.588%
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+6.57%
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+H3K27me3
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+18139
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+18967
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+11.1%
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+22.5%
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\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 "tab:peak-calling-summary"
+
+\end_inset
+
+SICER+IDR peak-calling summary
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Figures 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:IDR-RC-H3K4me2"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+, 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:IDR-RC-H3K4me3"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+, and 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:IDR-RC-H3K27me3"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+ show the IDR rank-consistency plots for peaks called in an arbitrarily-chosen
+ pair of donors.
+ For all 3 histone marks, when the peaks for each donor are ranked according
+ to their scores, SICER produces much more reproducible results between
+ donors.
+ This is consistent with SICER's stated goal of identifying broad peaks,
+ in contrast to MACS, which is designed for identifying sharp peaks.
+ Based on this observation, the SICER peak calls were used for all downstream
+ analyses that involved ChIP-seq peaks.
+ Table 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "tab:peak-calling-summary"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+ gives a summary of the peak calling statistics for each histone mark.
+\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/Promoter Peak Distance Profile-PAGE1-CROP.pdf
+	width 100col%
+	groupId colwidth
+
+\end_inset
+
+
 \end_layout
 
-\begin_deeper
-\begin_layout Itemize
-Compare peak sizes and number of called peaks
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+
+\series bold
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:effective-promoter-radius"
+
+\end_inset
+
+Enrichment of peaks in promoter neighborhoods.
 \end_layout
 
-\begin_layout Itemize
-Show representative IDR consistency plots for both
+\end_inset
+
+
 \end_layout
 
-\end_deeper
-\begin_layout Itemize
-IDR analysis shows that SICER-called peaks are much more reproducible between
- biological replicates
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Itemize
 Each histone mark is enriched within a certain radius of gene TSS positions,
- but that radius is different for each mark (figure)
+ but that radius is different for each mark (figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:effective-promoter-radius"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+, previously in 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "LaMere2016"
+literal "false"
+
+\end_inset
+
+ Fig.
+ S2)
+\end_layout
+
+\begin_layout Subsection
+RNA-seq align+quant method selection
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Maybe fix up the axis ranges for these plots?
+\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/rnaseq-compare/ensmebl-vs-entrez-star-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
+Comparison of STAR quantification between Ensembl and Entrez gene identifiers
+\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 collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/rnaseq-compare/ensmebl-vs-entrez-shoal-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
+Comparison of Salmon+Shoal quantification between Ensembl and Entrez gene
+ identifiers
+\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/rnaseq-compare/star-vs-hisat2-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
+Comparison of quantification between STAR and HISAT2 for identical annotation
+\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/rnaseq-compare/star-vs-salmon-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
+Comparison of quantification between STAR and Salmon for identical annotation
+\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/rnaseq-compare/salmon-vs-kallisto-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
+Comparison of quantification between Salmon and Kallisto for identical annotatio
+n
+\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/rnaseq-compare/salmon-vs-shoal-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
+Comparison of quantification between Salmon with and without Shoal for identical
+ annotation
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+
 \end_layout
 
 \begin_layout Subsection
@@ -996,7 +1725,7 @@ This section could probably use some citations
 \end_layout
 
 \begin_layout Standard
-Microarrays, bead ararys, and similar assays produce raw data in the form
+Microarrays, bead arrays, and similar assays produce raw data in the form
  of fluorescence intensity measurements, with the each intensity measurement
  proportional to the abundance of some fluorescently-labelled target DNA
  or RNA sequence that base pairs to a specific probe sequence.