diff --git a/DDV/Ideogram.py b/DDV/Ideogram.py index 338d9a9..891f4f4 100644 --- a/DDV/Ideogram.py +++ b/DDV/Ideogram.py @@ -204,6 +204,8 @@ def increment(digits, radices, place): # [5,5,5,5,5 ,53], 1, 1)) # layout = Ideogram([3,3,3,3,3,27], # thin layout # [3,3,3,3,3,3 ,53], 1, 1) + # 3*3*3*3*3*27* + # 3*3*3*3*3 = 1,594,323 bp per fiber row radix_settings = eval(sys.argv[2]) assert len(radix_settings) == 4 and \ diff --git a/DDV/OutlinedAnnotation.py b/DDV/OutlinedAnnotation.py index 1abc6e7..1d0a260 100644 --- a/DDV/OutlinedAnnotation.py +++ b/DDV/OutlinedAnnotation.py @@ -63,33 +63,38 @@ def draw_extras(self): self.draw_annotation_labels(markup_image, annotated_regions, universal_prefix) self.image = Image.alpha_composite(self.image, markup_image) - def draw_annotation_outlines(self, annotations, markup_canvas, shadow): + def draw_annotation_outlines(self, annotations, markup_canvas, shadow_color): regions = self.find_annotated_regions(annotations) - print("Drawing annotation outlines") - # desaturated purple drop shadow, decreasing opacity - opacities = linspace(197, 10, self.border_width) - outline_colors = [(shadow[0], shadow[1], shadow[2], int(opacity)) for opacity in opacities] - - exon_color = (255,255,255,107) # white highlighter. This is less disruptive overall - for region in regions: - for point in region.exon_region_points(): # highlight exons - blend_pixel(markup_canvas, point, exon_color) + self.draw_exons(markup_canvas, regions) + annotation_point_union = self.draw_big_shadow_outline(markup_canvas, regions, shadow_color) + self.draw_secondary_shadows(annotation_point_union, markup_canvas, regions, shadow_color) + return regions + def draw_big_shadow_outline(self, markup_canvas, regions, shadow): + print("Drawing annotation outlines") annotation_point_union = set() for region in regions: annotation_point_union.update(region.points) region.outline_points = outlines(region.points, # small outline - self.border_width // 4, self.image.width, self.image.height) - + self.border_width // 4, self.image.width, self.image.height) + # desaturated purple drop shadow, decreasing opacity + opacities = linspace(197, 10, self.border_width) + outline_colors = [(shadow[0], shadow[1], shadow[2], int(opacity)) for opacity in opacities] big_shadow = outlines(annotation_point_union, - self.border_width, self.image.width, self.image.height) + self.border_width, self.image.width, self.image.height) self.draw_shadow(big_shadow, markup_canvas, outline_colors) - self.draw_secondary_shadows(annotation_point_union, markup_canvas, regions, shadow) + return annotation_point_union - return regions + def draw_exons(self, markup_canvas, regions): + print("Drawing exons") + exon_color = (255, 255, 255, 107) # white highlighter. This is less disruptive overall + for region in regions: + for point in region.exon_region_points(): # highlight exons + blend_pixel(markup_canvas, point, exon_color) def draw_secondary_shadows(self, annotation_point_union, markup_canvas, regions, shadow): """Find subset of genes who are completely overshadowed""" + print("Drawing secondary shadows") opacities = linspace(170, 40, self.border_width // 4) outline_colors = [(shadow[0], shadow[1], shadow[2], int(opacity)) for opacity in opacities] for region in regions: @@ -158,7 +163,11 @@ def draw_annotation_labels(self, markup_image, annotated_regions, universal_pref if vertical_label: width, height = height, width # swap - font_size = max(9, int((width * 0.09) - 0)) # found eq with two reference points + font_size_by_width = max(9, int((min(3000, width) * 0.09))) # found eq with two reference points + font_size_by_height = max(9, int((min(3000, height * 18) * 0.09))) + if height <= 244: # 398580bp = 1900 width, 243 height + font_size_by_height = min(font_size_by_height, int(1900 * .09)) # 171 max font size in one fiber + font_size = min(font_size_by_width, font_size_by_height) if height < 11: height = 11 # don't make the area so small it clips the text upper_left[1] -= 2 @@ -215,27 +224,23 @@ def write_label(self, contig_name, width, height, font_size, title_width, upper_ canvas.paste(txt, (upper_left[0], upper_left[1]), txt) -def getNeighbors(pt): - return {(pt[0] + 1, pt[1]), (pt[0] - 1, pt[1]), (pt[0], pt[1] + 1), (pt[0], pt[1] - 1)} +def getNeighbors(x, y): + return (x + 1, y), (x - 1, y), (x, y + 1), (x, y - 1) -def allNeighbors(pt): - return getNeighbors(pt).union({(pt[0] + 1, pt[1] + 1), (pt[0] - 1, pt[1] - 1), - (pt[0] - 1, pt[1] + 1), (pt[0] + 1, pt[1] - 1)}) +def allNeighbors(x, y): + return set(getNeighbors(x, y)).union({(x + 1, y + 1), (x - 1, y - 1), + (x - 1, y + 1), (x + 1, y - 1)}) -def outlines(annotation_points, radius, width, height, square_corners=False): - workingSet = set() - nextEdge = set() - workingSet.update(annotation_points) - nextEdge.update(annotation_points) +def outlines(annotation_points, radius, width, height): + workingSet = set(annotation_points) + nextEdge = set(annotation_points) layers = [] for iterationStep in range(radius, 0, -1): activeEdge = nextEdge nextEdge = set() - - for block in activeEdge: - neighbors = allNeighbors(block) if square_corners else getNeighbors(block) - for n in neighbors: - if n not in workingSet and width > n[0] > 0 and height > n[1] > 0 : # TODO: check in bounds + for pt in activeEdge: + for n in getNeighbors(pt[0], pt[1]): + if n not in workingSet and width > n[0] > 0 and height > n[1] > 0: # TODO: check in bounds workingSet.add(n) nextEdge.add(n) layers.append(nextEdge) @@ -255,15 +260,15 @@ def __init__(self, GFF_annotation, renderer, xy_seq_start): self.protein_spans = [] def exon_region_points(self): - exon_indices = [] - for i in range(self.start, self.end): - if any([i in exon for exon in self.protein_spans]): - exon_indices.append(i) + exon_indices = set() + for exon in self.protein_spans: + exon_indices.update(exon.set_of_points()) + length = len(self.points) exon_points = [] for i in exon_indices: - if 0 <= i - self.start < len(self.points): - exon_points.append(self.points[i - self.start]) - # introns = [i for span in self.non_protein_spans for i in range(span.begin, span.end)] + adjusted = i - self.start + if 0 <= adjusted < length: + exon_points.append(self.points[adjusted]) return exon_points def add_cds_region(self, annotation_entry): diff --git a/DDV/Span.py b/DDV/Span.py index 790fbf5..18eb421 100644 --- a/DDV/Span.py +++ b/DDV/Span.py @@ -102,6 +102,9 @@ def sample(self, sequence, error_gap_okay=True): else: raise e + def set_of_points(self): + return set(range(self.begin, self.end)) + class AlignedSpans(object):