Darkened borders of 4-1 & 4-3.

OuhscBbmc · Feb 8, 2015 · 4dc2b0a · 4dc2b0a
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Showing 19 changed files with 38 additions and 36 deletions.
diff --git a/Chapter04/Chapter04.R b/Chapter04/Chapter04.R
@@ -47,7 +47,7 @@ dsFibromyalgiaT1Control <- dsFibromyalgiaT1Control[order(dsFibromyalgiaT1Control
 ## @knitr Figure04_01
 breaksX <- seq(from=7, to=23, by=1)
 histogramX <- ggplot(dsFibromyalgiaT1Control, aes(x=X)) +
-  geom_histogram(breaks=breaksX, fill=PaletteControlPsqi[1], color="gray95", alpha=.6) + 
+  geom_histogram(breaks=breaksX, fill=PaletteControlPsqiLight[1], color=PaletteControlPsqiDark[2], alpha=.6) + 
   chapterTheme +
   theme(panel.grid.minor=element_blank()) +
   theme(panel.grid.major.x=element_blank()) +
@@ -125,7 +125,7 @@ histogramXInset <- histogramX + scale_x_continuous(breaks=breaksXSparse) + labs(
 
 
 # histogramZInset <- ggplot(dsFibromyalgiaT1Control, aes(x=Z)) +
-#   geom_histogram(breaks=breaksZ, fill=PaletteControlPsqi[2], color="gray95", alpha=.6) + 
+#   geom_histogram(breaks=breaksZ, fill=PaletteControlPsqiLight[2], color="gray95", alpha=.6) + 
 #   labs(x="Z", y=NULL) + 
 #   chapterTheme +
 #   theme(panel.grid.minor=element_blank()) +
@@ -135,7 +135,7 @@ histogramXInset <- histogramX + scale_x_continuous(breaks=breaksXSparse) + labs(
 
 # ggplot(dsFibromyalgiaT1Control, aes(x=X)) +
 #   #   geom_histogram(breaks=breaksX, fill="#037995", color="gray95", alpha=.6) + 
-#   geom_histogram(breaks=breaksX-.01, fill=PaletteControlPsqi[2], color="gray95", alpha=.6) + 
+#   geom_histogram(breaks=breaksX-.01, fill=PaletteControlPsqiLight[2], color="gray95", alpha=.6) + 
 # #   scale_x_continuous(breaks=breaksXSparse, labels=round(breaksZSparse, 2)) + 
 #   labs(x="Z", y=NULL) + 
 #   chapterTheme +
@@ -146,7 +146,7 @@ histogramXInset <- histogramX + scale_x_continuous(breaks=breaksXSparse) + labs(
 
 histogramZInset <- ggplot(dsFibromyalgiaT1Control, aes(x=X)) +
   #   geom_histogram(breaks=breaksX, fill="#037995", color="gray95", alpha=.6) + 
-  geom_histogram(breaks=breaksX, fill=PaletteControlPsqi[2], color="gray95", alpha=.6) + 
+  geom_histogram(breaks=breaksX, fill=PaletteControlPsqiLight[2], color=PaletteControlPsqiDark[2], alpha=.6) + 
   scale_x_continuous(breaks=breaksXSparse, labels=round(breaksZSparse, 2)) + 
   chapterTheme +
   theme(panel.grid.minor=element_blank()) +

diff --git a/Chapter04/Chapter04.html b/Chapter04/Chapter04.html
diff --git a/Chapter04/Chapter04.md b/Chapter04/Chapter04.md
@@ -20,11 +20,11 @@ opts_chunk$set(
   fig.height = 4, 
   fig.width = 5.5, 
   out.width = "550px", #This affects only the markdown, not the underlying png file.  The height will be scaled appropriately.
-#   fig.path = 'figure_rmd/',     
-#   dev = "png",
-#   dpi = 400
-  fig.path = 'figure_pdf/',     
-  dev = "pdf"#,
+  fig.path = 'figure_rmd/',     
+  dev = "png",
+  dpi = 400
+  # fig.path = 'figure_pdf/',     
+  # dev = "pdf"#,
   # dev.args=list(pdf = list(colormodel = 'cmyk'))
 )
 echoChunks <- FALSE
@@ -47,42 +47,42 @@ read_chunk("./Chapter04/Chapter04.R")
 
 
 ## Figure 4-1
-<img src="figure_pdf/Figure04_01-1.pdf" title="" alt="" width="550px" />
+<img src="figure_rmd/Figure04_01-1.png" title="" alt="" width="550px" />
 
 ## Figure 4-2
-<img src="figure_pdf/Figure04_02-1.pdf" title="" alt="" width="550px" />
+<img src="figure_rmd/Figure04_02-1.png" title="" alt="" width="550px" />
 
 ## Figure 4-3
-<img src="figure_pdf/Figure04_03-1.pdf" title="" alt="" width="550px" />
+<img src="figure_rmd/Figure04_03-1.png" title="" alt="" width="550px" />
 
 ## Figure 4-4
-<img src="figure_pdf/Figure04_04-1.pdf" title="" alt="" width="550px" />
+<img src="figure_rmd/Figure04_04-1.png" title="" alt="" width="550px" />
 
 ## Figure 4-5
-<img src="figure_pdf/Figure04_05-1.pdf" title="" alt="" width="550px" />
+<img src="figure_rmd/Figure04_05-1.png" title="" alt="" width="550px" />
 
 ## Figure 4-6
 See Table A: Standard normal distribution.
 
 ## Figures 4-7
-<img src="figure_pdf/Figure04_07-1.pdf" title="" alt="" width="300px" />
+<img src="figure_rmd/Figure04_07-1.png" title="" alt="" width="300px" />
 
 ## Figure 4-8
-<img src="figure_pdf/Figure04_08-1.pdf" title="" alt="" width="350px" /><img src="figure_pdf/Figure04_08-2.pdf" title="" alt="" width="350px" />
+<img src="figure_rmd/Figure04_08-1.png" title="" alt="" width="350px" /><img src="figure_rmd/Figure04_08-2.png" title="" alt="" width="350px" />
 
 ## Figure 4-9
-<img src="figure_pdf/Figure04_09-1.pdf" title="" alt="" width="550px" />
+<img src="figure_rmd/Figure04_09-1.png" title="" alt="" width="550px" />
 
 ## Unused Graphics
-<img src="figure_pdf/UnusedVariantsFigure04_04-1.pdf" title="" alt="" width="550px" /><img src="figure_pdf/UnusedVariantsFigure04_04-2.pdf" title="" alt="" width="550px" /><img src="figure_pdf/UnusedVariantsFigure04_04-3.pdf" title="" alt="" width="550px" />
-<img src="figure_pdf/UnusedVariantsFigure04_08-1.pdf" title="" alt="" width="550px" />
+<img src="figure_rmd/UnusedVariantsFigure04_04-1.png" title="" alt="" width="550px" /><img src="figure_rmd/UnusedVariantsFigure04_04-2.png" title="" alt="" width="550px" /><img src="figure_rmd/UnusedVariantsFigure04_04-3.png" title="" alt="" width="550px" />
+<img src="figure_rmd/UnusedVariantsFigure04_08-1.png" title="" alt="" width="550px" />
 
 ## Session Info
 For the sake of documentation and reproducibility, the current report was build on a system using the following software.
 
 
 ```
-Report created by wibeasley at 2015-02-08, 00:16 -0600
+Report created by wibeasley at 2015-02-08, 14:58 -0600
 ```
 
 ```

diff --git a/Chapter04/figure_pdf/Figure04_01-1.pdf b/Chapter04/figure_pdf/Figure04_01-1.pdf
diff --git a/Chapter04/figure_pdf/Figure04_02-1.pdf b/Chapter04/figure_pdf/Figure04_02-1.pdf
diff --git a/Chapter04/figure_pdf/Figure04_03-1.pdf b/Chapter04/figure_pdf/Figure04_03-1.pdf
diff --git a/Chapter04/figure_pdf/Figure04_04-1.pdf b/Chapter04/figure_pdf/Figure04_04-1.pdf
diff --git a/Chapter04/figure_pdf/Figure04_05-1.pdf b/Chapter04/figure_pdf/Figure04_05-1.pdf
diff --git a/Chapter04/figure_pdf/Figure04_07-1.pdf b/Chapter04/figure_pdf/Figure04_07-1.pdf
diff --git a/Chapter04/figure_pdf/Figure04_08-1.pdf b/Chapter04/figure_pdf/Figure04_08-1.pdf
diff --git a/Chapter04/figure_pdf/Figure04_08-2.pdf b/Chapter04/figure_pdf/Figure04_08-2.pdf
diff --git a/Chapter04/figure_pdf/Figure04_09-1.pdf b/Chapter04/figure_pdf/Figure04_09-1.pdf
diff --git a/Chapter04/figure_pdf/UnusedVariantsFigure04_04-1.pdf b/Chapter04/figure_pdf/UnusedVariantsFigure04_04-1.pdf
diff --git a/Chapter04/figure_pdf/UnusedVariantsFigure04_04-2.pdf b/Chapter04/figure_pdf/UnusedVariantsFigure04_04-2.pdf
diff --git a/Chapter04/figure_pdf/UnusedVariantsFigure04_04-3.pdf b/Chapter04/figure_pdf/UnusedVariantsFigure04_04-3.pdf
diff --git a/Chapter04/figure_pdf/UnusedVariantsFigure04_08-1.pdf b/Chapter04/figure_pdf/UnusedVariantsFigure04_08-1.pdf
diff --git a/Chapter04/figure_rmd/Figure04_01-1.png b/Chapter04/figure_rmd/Figure04_01-1.png
diff --git a/Chapter04/figure_rmd/Figure04_03-1.png b/Chapter04/figure_rmd/Figure04_03-1.png
diff --git a/CommonCode/BookTheme.R b/CommonCode/BookTheme.R
@@ -51,7 +51,9 @@ PaletteObesityState <- transformColor(adjustcolor(brewer.pal(5, "Dark2"))[c(2,3)
 PaletteWorldDeathsRestricted <- transformColor(c("#497862", "#A54891")) #Hand-picked
 PaletteWorldDeathsRestrictedFaint <- transformColor(adjustcolor(PaletteWorldDeathsRestricted, alpha.f=.2))
 
-PaletteControlPsqi <- transformColor(c("#1A7F7C", "#1595B2")) #From http://colrd.com/palette/22521/; http://colrd.com/palette/18981/
+PaletteControlPsqiLight <- transformColor(c("#1A7F7C", "#1595B2")) #From http://colrd.com/palette/22521/; http://colrd.com/palette/18981/
+PaletteControlPsqiDark <- transformColor(c("#215f5c", "#225a88")) #From http://colrd.com/palette/22521/; http://colrd.com/palette/18981/
+#
 
 #Use the same palette as the crit graphs in Chapters 10-12.
 #  * Purple is the distribution line