Improve K-means slides

Snakefile

@@ -352,6 +352,14 @@ rule svg_raster:
         outfile = os.path.join(os.path.abspath("."), output[0])
         shell('''inkscape {infile:q} --export-png={outfile:q} --export-dpi=300''')
 
+rule png_rotate:
+    input: 'graphics/{filename}.png'
+    output: 'graphics/{filename}-ROT{angle,[1-9][0-9]*}.png'
+    run:
+        if re.search('-ROT[1-9][0-9]*$', wildcards.filename):
+            raise ValueError("Cannot double-rotate")
+        shell('convert {input:q} -rotate {wildcards.angle:q} {output:q}')
+
 rule R_to_html:
     '''Render an R script as syntax-hilighted HTML.'''
     input: '{dirname}/{basename}.R'
@@ -383,7 +391,6 @@ rule build_presentation_beamer:
         if PDFINFO_PATH:
             shell('''{PDFINFO_PATH} {output.pdf:q}''')
 
-
 rule build_presentation_ppt:
     input:
         extra_preamble='extra-preamble.latex',

presentation.mkdn

@@ -254,39 +254,81 @@ presence or absence anywhere within the promoter?
   
 ## H3K4me2 promoter neighborhood K-means clusters
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-clusters-CROP.png)
+![Cluster means for H3K4me2](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-clusters-CROP.png)
 
 ## H3K4me2 promoter neighborhood cluster PCA
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-PCA-CROP.png)
+::::: {.columns}
+::: {.column width="50%"}
+![Cluster means for H3K4me2](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-clusters-CROP.png)
+:::
+::: {.column width="50%"}
+![PCA plot of promoters](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-PCA-CROP.png)
+:::
+:::::
 
 ## H3K4me2 promoter neighborhood cluster expression
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-expression-CROP.png)
+::::: {.columns}
+::: {.column width="50%"}
+![Cluster means for H3K4me2](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-clusters-CROP.png)
+:::
+::: {.column width="50%"}
+![Cluster expression distributions](graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-expression-CROP-ROT90.png)
+:::
+:::::
 
 ## H3K4me3 promoter neighborhood K-means clusters
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-clusters-CROP.png)
+![Cluster means for H3K4me3](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-clusters-CROP.png)
 
-## H3K4me3 promoter neighborhood cluster PCA
+## H3K4me3 promoter neighborhood K-means clusters
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-PCA-CROP.png)
+::::: {.columns}
+::: {.column width="50%"}
+![Cluster means for H3K4me3](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-clusters-CROP.png)
+:::
+::: {.column width="50%"}
+![PCA plot of promoters](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-PCA-CROP.png)
+:::
+:::::
 
 ## H3K4me3 promoter neighborhood cluster expression
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-expression-CROP.png)
+::::: {.columns}
+::: {.column width="50%"}
+![Cluster means for H3K4me3](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-clusters-CROP.png)
+:::
+::: {.column width="50%"}
+![Cluster expression distributions](graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-expression-CROP-ROT90.png)
+:::
+:::::
 
 ## H3K27me3 promoter neighborhood K-means clusters
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-clusters-CROP.png)
+![Cluster means for H3K27me3](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-clusters-CROP.png)
 
-## H3K27me3 promoter neighborhood cluster PCA
+## H3K27me3 promoter neighborhood K-means clusters
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-PCA-CROP.png)
+::::: {.columns}
+::: {.column width="50%"}
+![Cluster means for H3K27me3](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-clusters-CROP.png)
+:::
+::: {.column width="50%"}
+![PCA plot of promoters](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-PCA-CROP.png)
+:::
+:::::
 
 ## H3K27me3 promoter neighborhood cluster expression
 
-![(Insert figure legend)](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-expression-CROP.png)
+::::: {.columns}
+::: {.column width="50%"}
+![Cluster means for H3K27me3](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-clusters-CROP.png)
+:::
+::: {.column width="50%"}
+![Cluster expression distributions](graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-expression-CROP-ROT90.png)
+:::
+:::::
 
 ## What have we learned?