瀏覽代碼

Add more plots, fixup citations, remove unneeded rasters

Ryan C. Thompson 5 年之前
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b12f8e1f2a

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graphics/presentation/CCF-plots-A.svg


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graphics/presentation/CCF-plots-B.svg


二進制
graphics/presentation/IDR-example.pdf


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graphics/presentation/SICER-fig1.svg

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二進制
graphics/presentation/kidney-graft-survival.png


+ 30 - 29
presentation.mkdn

@@ -14,7 +14,7 @@ fontsize: 14pt
 
 ::: incremental
 
-* 36,528 transplants performed in the USA in 2018[^1]
+* 36,528 transplants performed in the USA in 2018[^organdonor]
 
 * 100 transplants every day!
 
@@ -23,13 +23,11 @@ fontsize: 14pt
 
 :::
 
-[^1]: [organdonor.gov](https://www.organdonor.gov/statistics-stories/statistics.html)
+[^organdonor]: [organdonor.gov](https://www.organdonor.gov/statistics-stories/statistics.html)
 
 ## Organ transplants are a life-saving treatment
 
-![Organ donation statistics for the USA in 2018[^2]](graphics/presentation/transplants-organ-CROP-RASTER.png){ height=70% }
-
-[^2]: [organdonor.gov](https://www.organdonor.gov/statistics-stories/statistics.html)
+![Organ donation statistics for the USA in 2018[^organdonor]](graphics/presentation/transplants-organ-CROP.pdf){ height=70% }
 
 ## Graft rejection is an adaptive immune response
 
@@ -52,9 +50,9 @@ fontsize: 14pt
 
 ## Allograft rejection remains a major long-term problem
 
-![Kidney allograft survival rates in children by transplant year[^3]](graphics/presentation/kidney-graft-survival.png){ height=65% }
+![Kidney allograft survival rates in children by transplant year[^kim-marks]](graphics/presentation/kidney-graft-survival.png){ height=65% }
 
-[^3]:[ Kim & Marks. "Long-term outcomes of children after solid organ transplantation". In: Clinics (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884158/?report=classic)
+[^kim-marks]:[ Kim & Marks. "Long-term outcomes of children after solid organ transplantation". In: Clinics (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884158/?report=classic)
 
 ## Rejection is treated with immune suppressive drugs
 
@@ -99,23 +97,23 @@ and memory $\mathsf{CD4}^{+}$ T-cell activation
 
 ## Memory cells: faster, stronger, and more independent
 
-![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-A-SVG.png)
+![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-A.svg)
 
 ## Memory cells: faster, stronger, and more independent
 
-![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-B-SVG.png)
+![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-B.svg)
 
 ## Memory cells: faster, stronger, and more independent
 
-![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-C-SVG.png)
+![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-C.svg)
 
 ## Memory cells: faster, stronger, and more independent
 
-![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-D-SVG.png)
+![Naïve and memory T-cell responses to activation](graphics/presentation/T-cells-D.svg)
 
 ## Memory cells are a problem for immune suppression
 
-<!-- Need graphics -->
+<!-- Need graphics? Or maybe just mark this slide as speaker notes for the previous one -->
 
 \large
 
@@ -179,41 +177,44 @@ Data generated by Sarah Lamere, published in GEO as
 
 ## Histone modifications occur on consecutive histones
 
-![ChIP-seq coverage in IL2 gene[^5]](graphics/presentation/LaMere-thesis-fig3.9-SVG-CROP.png){ height=70% }
+![ChIP-seq coverage in IL2 gene[^lamerethesis]](graphics/presentation/LaMere-thesis-fig3.9-SVG-CROP.pdf){ height=70% }
 
-[^5]: Sarah LaMere. "Dynamic epigenetic regulation of CD4 T cell activation and memory formation". PhD thesis. TSRI, 2015.
+[^lamerethesis]: Sarah LaMere. "Dynamic epigenetic regulation of CD4 T cell activation and memory formation". PhD thesis. TSRI, 2015.
 
 ## Histone modifications occur on consecutive histones
 
-![Strand cross-correlation plots](graphics/CD4-csaw/csaw/CCF-plots-PAGE2-CROP-RASTER.png)
+![Strand cross-correlation plots](graphics/presentation/CCF-plots-A-SVG.pdf)
 
-## Finding enriched regions across the genome
+## Histone modifications occur on consecutive histones
+
+![Strand cross-correlation plots](graphics/presentation/CCF-plots-B-SVG.pdf)
+
+## SICER identifies enriched regions across the genome
+
+![Finding "islands" of coverage with SICER[^sicer]](graphics/presentation/SICER-fig1.svg)
+
+[^sicer]: [Chongzhi Zang et al. “A clustering approach for identification of enriched domains from histone modification ChIP-Seq data”. In: Bioinformatics 25.15 (2009) doi: 10.1093/bioinformatics/btp340.](https://doi.org/10.1093/bioinformatics/btp340)
 
-<!-- Graphic from SICER paper: Fig1 -->
-<!-- Use one of my IDR example plots for IDR -->
+## IDR identifies *reproducible* enriched regions
 
-* Scan across the genome looking for regions with read coverage above
-  background level in each donor using SICER peak caller[^6]
-* Use Irreducible Discovery Rate framework to identify peaks that are
-  called consistently across multiple donors[^7]
+![Example irreproducible discovery rate[^idr] score consistency plot](graphics/presentation/IDR-example-CROP-RASTER.png)
 
-[^6]: [Chongzhi Zang et al. “A clustering approach for identification of enriched domains from histone modification ChIP-Seq data”. In: Bioinformatics 25.15 (2009) doi: 10.1093/bioinformatics/btp340.](https://doi.org/10.1093/bioinformatics/btp340)
-[^7]: [Qunhua Li et al. “Measuring reproducibility of high-throughput experiments”. In: AOAS (2011)](https://doi.org/10.1214/11-AOAS466)
+[^idr]: [Qunhua Li et al. “Measuring reproducibility of high-throughput experiments”. In: AOAS (2011)](https://doi.org/10.1214/11-AOAS466)
 
 ## Finding enriched regions across the genome
 
-![Peak-calling summary statistics](graphics/presentation/RCT-thesis-table2.2-SVG-CROP.png)
+![Peak-calling summary statistics](graphics/presentation/RCT-thesis-table2.2-SVG.pdf)
 
 
 ## Each histone mark has an "effective promoter radius"
 
-![Enrichment of peaks near promoters](graphics/CD4-csaw/Promoter-Peak-Distance-Profile-PAGE1-CROP-RASTER.png)
+![Enrichment of peaks near promoters](graphics/CD4-csaw/Promoter-Peak-Distance-Profile-PAGE1-CROP.pdf)
 
 ## Peaks in promoters correlate with gene expression
 
 <!-- TODO: Pull out one column and rotate it -->
 
-![Expression distributions of genes with and without promoter peaks](graphics/CD4-csaw/FPKM-by-Peak-Violin-Plots-CROP-RASTER.png)
+![Expression distributions of genes with and without promoter peaks](graphics/CD4-csaw/FPKM-by-Peak-Violin-Plots-CROP.pdf)
 
 ## The story so far
 
@@ -288,7 +289,7 @@ presence or absence anywhere within the promoter?
 
 ## Differential modification disappears by Day 14
 
-![Differential modification between naïve and memory samples at each time point](graphics/presentation/RCT-thesis-table2.4-SVG-CROP.png)
+![Differential modification between naïve and memory samples at each time point](graphics/presentation/RCT-thesis-table2.4-SVG-CROP.pdf)
 
 ## Convergence at Day 14 H3K4me2
 
@@ -327,7 +328,7 @@ presence or absence anywhere within the promoter?
 
 <!-- ## Slide -->
 
-<!-- ![(Insert figure legend)](graphics/CD4-csaw/LaMere2016_fig8-RASTER.png) -->
+<!-- ![(Insert figure legend)](graphics/CD4-csaw/LaMere2016_fig8.pdf) -->
 
 
 ## Takeaway 1: Each histone mark has an "effective promoter radius"

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