Supp viz

example/example.smk

@@ -105,5 +105,8 @@ rule all:
     'results/figure_combined.pdf',
     'results/figure_combined.png',
     'results/figure_combined.tiff',
+    'results/supplemental_figure_combined.pdf',
+    'results/supplemental_figure_combined.png',
+    'results/supplemental_figure_combined.tiff',
     # Sample information
     'results/sample_stats.tsv'

example/rules/deeptools.smk

@@ -95,6 +95,7 @@ rule computeMatrix_chip:
     shell:'''
     computeMatrix {params.mattype} -p {threads} \
       -S {params.bws} \
+    'results/supplemental_figure_combined.pdf',
       -o {output.mat} \
       -bs {params.binsize} \
       --missingDataAsZero \
@@ -156,13 +157,98 @@ rule plotHeatmap_atac:
         runtime = 1440
     shell:'''
     plotHeatmap -m {input.mat} -out {output.png} \
-    --startLabel "\\-5kb" --endLabel "\\+5kb" --colorMap Reds \
+      --startLabel "\\-5kb" \
+      --endLabel "\\+5kb" \
+      --colorMap Reds \
       --xAxisLabel "" \
       --interpolationMethod bilinear \
       --regionsLabel up down non-de \
       --whatToShow "heatmap and colorbar"
     '''
 
+rule multiBigwigSummary_ATAC:
+    input:
+        bw = expand('results/atac/{atacsample}.bw', atacsample=ATACSAMPLES)
+    output:
+        npz = 'results/atac_summ.npz'
+    threads: 10
+    params:
+        labels = lambda wildcards, input: ' '.join( [i.split('_')[2] + '-' + i.split('_')[4] for i in input.bw] )
+    resources:
+        mem_mb = 8000,
+        runtime = 1440
+    shell:'''
+    multiBigwigSummary bins \
+      -p {threads} \
+      -o {output.npz} \
+      -b {input.bw} \
+      --labels {params.labels} 
+    '''
+
+rule plotPCA_ATAC:
+    input:
+        mat = 'results/atac_summ.npz'
+    output:
+        png = 'results/atac_pca.png'
+    resources:
+        mem_mb = 4000,
+        runtime = 1440
+    shell:'''
+    plotPCA \
+      -in {input.mat} \
+      -o {output.png} \
+      --colors blue blue red red \
+      --plotWidth 6 \
+      --plotHeight 12 \
+      --addLabels 
+    '''
+
+rule plotCorrelation_ATAC:
+    input:
+        mat = 'results/atac_summ.npz'
+    output:
+        png = 'results/atac_correlation.png'
+    resources:
+        mem_mb = 4000,
+        runtime = 1440
+    shell:'''
+    plotCorrelation \
+      -in {input.mat} \
+      -o {output.png} \
+      --corMethod pearson \
+      --whatToPlot heatmap \
+      --colorMap RdYlBu \
+      --plotNumbers \
+      --skipZeros \
+      --plotWidth 6 \
+      --plotHeight 6
+    '''
+
+rule plotEnrichment_ATAC:
+    input:
+        bams = expand('deeptools_input/{atacsample}.bam', atacsample=ATACSAMPLES),
+        bed = 'deeptools_input/upreg_ATAC.bed'
+    output:
+        png = 'results/atac_enrichment.png'
+    params:
+        labels = lambda wildcards, input: ' '.join( [i.split('_')[2] + '-' + i.split('_')[4] for i in input.bams] )
+    threads: 10
+    resources:
+        mem_mb = 4000,
+        runtime = 1440
+    shell:'''
+    plotEnrichment \
+      -p {threads} \
+      -b {input.bams} \
+      -o {output.png} \
+      --BED {input.bed} \
+      --labels {params.labels}  \
+      --colors blue blue red red \
+      --plotWidth 6 \
+      --plotHeight 6 \
+      --variableScales
+    '''    
+
 rule computeMatrix_meth:
     input:
         bw = expand('deeptools_input/{bssample}_CpG.bw', bssample=BSSAMPLES),
@@ -225,3 +311,18 @@ rule combine_figure:
         runtime = 60
     script:
         'scripts/combined_figure.py'
+
+rule combine_supplemental_figure:
+    input:
+        atac_pca = 'results/atac_pca.png',
+        atac_corr = 'results/atac_correlation.png',
+        atac_enrich = 'results/atac_enrichment.png'
+    output:
+        pdf = 'results/supplemental_figure_combined.pdf',
+        png = 'results/supplemental_figure_combined.png',
+        tiff = 'results/supplemental_figure_combined.tiff'
+    resources:
+        mem_mb = 4000,
+        runtime = 60
+    script:
+        'scripts/combined_supplemental_figure.py'

example/rules/scripts/combined_supplemental_figure.py

@@ -0,0 +1,37 @@
+# Script to combine the 3 ATAC supplemental figures into a single figure
+
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+
+# Section 1: Read the images
+fig1 = mpimg.imread('results/atac_pca.png')
+fig2 = mpimg.imread('results/atac_correlation.png')
+fig3 = mpimg.imread('results/atac_enrichment.png')
+
+
+# Section 2: Create a new figure and add subplots
+# Plot 1
+ax1 = plt.subplot2grid((2, 2), (0, 0), rowspan=2)
+ax1.imshow(fig1)
+
+# Plot 2
+ax2 = plt.subplot2grid((2, 2), (0, 1), colspan=1)
+ax2.imshow(fig2)
+
+# Plot 3
+ax3 = plt.subplot2grid((2, 2), (1, 1), colspan=1)
+ax3.imshow(fig3)
+
+# Add titles to each subplot
+ax1.set_title('A', loc='left')
+ax2.set_title('B', loc='left')
+ax3.set_title('C', loc='left')
+
+# remove axes for all subplots
+for ax in [ax1, ax2, ax3]:
+    ax.axis('off')
+
+# save the combined figure
+plt.savefig('results/supplemental_figure_combined.png', dpi=300, bbox_inches='tight')
+plt.savefig('results/supplemental_figure_combined.pdf', dpi=300, bbox_inches='tight')
+plt.savefig('results/supplemental_figure_combined.tiff', dpi=300, bbox_inches='tight')

figures/collate_figures.sh

@@ -17,3 +17,7 @@ cp "$SCRIPT_DIR/../benchmark/results/performance.pdf" "$SCRIPT_DIR/figure2.pdf"
 ## Figure 4 - example (generated before, results committed to repo)cp
 cp "$SCRIPT_DIR/../example/results/figure_combined.png" "$SCRIPT_DIR/figure4.png"
 cp "$SCRIPT_DIR/../example/results/figure_combined.pdf" "$SCRIPT_DIR/figure4.pdf"
+
+## Supp. Figure - supplemental figure (generated before, results committed to repo)
+cp "$SCRIPT_DIR/../example/results/supplemental_figure_combined.png" "$SCRIPT_DIR/supp_figure1.png"
+cp "$SCRIPT_DIR/../example/results/supplemental_figure_combined.pdf" "$SCRIPT_DIR/supp_figure1.pdf"