#81 Packed layout: I found that less padding is better for keeping vi…

…sual patterns coherent over clusters of columns. The white space has a disproportionate effect if you space it out too much.
josiahseaman · Sep 18, 2019 · 353b37e · 353b37e
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commit 353b37e
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Showing 2 changed files with 26 additions and 20 deletions.
diff --git a/DDV/ParallelGenomeLayout.py b/DDV/ParallelGenomeLayout.py
@@ -28,16 +28,18 @@ def __init__(self, n_genomes, low_contrast=False, base_width=100, column_widths=
             column_widths = [self.base_width] * n_genomes
 
         self.each_layout = []  # one layout per data source assumed same order as self.fasta_sources
-        p = 6  # padding_between_layouts
+        # I found that less padding is better for keeping visual patterns coherent over clusters
+        # of columns.  The white space has a disproportionate effect if you space it out too much.
+        p = 1  # padding_between_layouts
         cluster_width = sum(column_widths) + p * n_genomes  # total thickness of data and padding
         cluster_width += p * 2  # double up on padding between super columns
-        column_clusters_per_mega_row = 10600 // cluster_width #10600
+        column_clusters_per_mega_row = 10600 // cluster_width  # 10600
 
         for nth_genome in range(n_genomes):
             all_columns_height = base_width * 10
-            standard_modulos = [column_widths[nth_genome], all_columns_height, column_clusters_per_mega_row, 10, 3, 4, 999]
+            standard_modulos = [column_widths[nth_genome], all_columns_height, column_clusters_per_mega_row, 12, 3, 4, 999]
             standard_step_pad = cluster_width - standard_modulos[0] + p
-            mega_row_padding = p * 3 + self.header_height
+            mega_row_padding = p * 3 + self.header_height + 10
             standard_padding = [0, 0, standard_step_pad, mega_row_padding, p*(3**2), p*(3**3), p*(3**4)]
             # steps inside a column bundle, not exactly the same as bundles steps
             thicknesses = [other_layout[0].modulo + p for other_layout in self.each_layout]
@@ -162,14 +164,14 @@ def calc_padding(self, total_progress, next_segment_length):
         if title_padding >= self.tile_label_size:
             title_padding = self.levels[2].chunk_size
         # Remove first title
-        if total_progress == 0:
-            # tail += title_padding  #commenting this out could cause problems with multiple contigs
-            title_padding = 0
-            if len(self.contigs) == 1:
-                tail = 0  # no need for tail
-            # i = min([i for i in range(len(self.levels)) if next_segment_length + 2600 < self.levels[i].chunk_size])
-            # total_padding = total_progress + title_padding + reset_padding + next_segment_length
-            # tail = self.levels[i - 1].chunk_size - total_padding % self.levels[i - 1].chunk_size - 1
+        # if total_progress == 0:
+        #     # tail += title_padding  #commenting this out could cause problems with multiple contigs
+        #     title_padding = 0
+        #     if len(self.contigs) == 1:
+        #         tail = 0  # no need for tail
+        #     i = min([i for i in range(len(self.levels)) if next_segment_length + 2600 < self.levels[i].chunk_size])
+        #     total_padding = total_progress + title_padding + reset_padding + next_segment_length
+        #     tail = self.levels[i - 1].chunk_size - total_padding % self.levels[i - 1].chunk_size - 1
 
         return reset_padding, title_padding, tail
 

diff --git a/DDV/UniqueAnnotation.ipynb b/DDV/UniqueAnnotation.ipynb
@@ -152,8 +152,8 @@
     "    name = s_chr.name.split('_')[0]\n",
     "    anno_contigs.append(Contig(name, ''.join(purged_a)))\n",
     "    seq_contigs.append(Contig(name, ''.join(purged_s)))\n",
-    "write_contigs_to_file('Human Unique Genes Gencode30.fa', anno_contigs)\n",
-    "write_contigs_to_file('Human Unique Sequence.fa', seq_contigs)"
+    "write_contigs_to_file(r\"E:\\Genomes\\Human\\Human Unique Genes Gencode30.fa\", anno_contigs)\n",
+    "write_contigs_to_file(r\"E:\\Genomes\\Human\\Human Unique Sequence.fa\", seq_contigs)"
    ]
   },
   {
@@ -208,24 +208,28 @@
    "source": []
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "source": [
+    "./FluentDNA --outname=\"Test chr21 unique annotation\" --fasta=\"E:\\Genomes\\Human\\gencode.v30.annotation.gff3__chr21.fa\" --chainfile=\"E:\\Genomes\\Human\\hg38ToPanTro6.over.chain\" --layout=unique --contigs chr21"
+   ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "./FluentDNA --outname=\"Test chr21 unique annotation\" --fasta=\"E:\\Genomes\\Human\\gencode.v30.annotation.gff3__chr21.fa\" --chainfile=\"E:\\Genomes\\Human\\hg38ToPanTro6.over.chain\" --layout=unique --contigs chr21"
+    "./FluentDNA --outname=\"Test chr21 unique seq\" --fasta=\"E:\\Genomes\\Human\\chroms\\chr21.fa\" --chainfile=\"E:\\Genomes\\Human\\hg38ToPanTro6.over.chain\" --layout=unique --contigs chr21"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "./FluentDNA --outname=\"Test chr21 unique seq\" --fasta=\"E:\\Genomes\\Human\\chroms\\chr21.fa\" --chainfile=\"E:\\Genomes\\Human\\hg38ToPanTro6.over.chain\" --layout=unique --contigs chr21"
+    "./FluentDNA --fasta=\"E:\\Genomes\\Human\\Human Unique Annotation merged.fa_squished.fa\"\n",
+    "--extrafastas\n",
+    "\"E:\\Genomes\\Human\\Human Unique Sequence.fa\"\n",
+    "--outname=\"Unique Human Genes and Centromere vs Chimpanzee PanTro6\"\n",
+    "--column_widths=\"[20,100]\""
    ]
   },
   {