def draw_gene_function_map(self, no_of_p_funcs_gene_no_go_no_list, go_no2index, function_name_region,\
output_fname, function_name_length, char_dimension, no_of_functions, font):
"""
10-31-05
11-28-05 draw_grid
2006-12-13 add font
"""
sys.stderr.write("Drawing gene_function_map...\n")
char_width, char_height = char_dimension
gene_no_repr_length = 0
for row in no_of_p_funcs_gene_no_go_no_list:
if len(repr(row[1]))>gene_no_repr_length:
gene_no_repr_length = len(repr(row[1]))
gene_no_repr_dimension = (char_width*gene_no_repr_length, char_height)
function_name_dimension = (char_width*function_name_length, char_height) #will rotate
no_of_p_funcs_repr_length = len(repr(no_of_p_funcs_gene_no_go_no_list[-1][0])) #-1 is the largest number
no_of_p_funcs_repr_dimension = (char_width*no_of_p_funcs_repr_length, char_height)
x_offset0 = 0
x_offset1 = gene_no_repr_dimension[0]
x_offset2 = x_offset1 + no_of_functions*function_name_dimension[1]
y_offset0 = 0
y_offset1 = function_name_dimension[0]
whole_dimension = (x_offset2+no_of_p_funcs_repr_dimension[0], \
y_offset1+len(no_of_p_funcs_gene_no_go_no_list)*gene_no_repr_dimension[1])
im = Image.new('RGB',(whole_dimension[0],whole_dimension[1]),(255,255,255))
draw = ImageDraw.Draw(im)
box = (x_offset1, y_offset0, x_offset2, y_offset1)
im.paste(function_name_region, box)
for i in range(len(no_of_p_funcs_gene_no_go_no_list)):
no_of_p_funcs, gene_no, go_no_set = no_of_p_funcs_gene_no_go_no_list[i]
y_offset_upper = y_offset1 + i*gene_no_repr_dimension[1]
y_offset_lower = y_offset_upper + gene_no_repr_dimension[1]
#draw gene_no
text_region = get_text_region(repr(gene_no), gene_no_repr_dimension, rotate=0, font=font)
box = (x_offset0, y_offset_upper, x_offset1, y_offset_lower)
im.paste(text_region, box)
#draw p_function
for go_no in go_no_set:
index = go_no2index[go_no]
x_offset_left = x_offset1 + index*function_name_dimension[1]
x_offset_right = x_offset_left + function_name_dimension[1]
draw.rectangle((x_offset_left, y_offset_upper, x_offset_right, y_offset_lower), fill=(0,255,0))
#draw no_of_p_funcs
text_region = get_text_region(repr(no_of_p_funcs), no_of_p_funcs_repr_dimension, rotate=0, font=font)
box = (x_offset2, y_offset_upper, whole_dimension[0], y_offset_lower)
im.paste(text_region, box)
#11-28-05
draw_grid(im, draw, [x_offset1, y_offset1, x_offset2, whole_dimension[1]], char_height, char_height)
im = im.rotate(270)
im.save(output_fname)
del im
sys.stderr.write("End drawing gene_function_map.\n")
def draw_tf_line(self, seq_name, seq_length, seq_strand, tf_info_list, tf_name2color, padding_width=5,\
padding_height=10, max_seq_name_length = 20, bs_width=1, im_10kb_length=800):
sys.stderr.write("\t Drawing tf_line")
char_width, char_height = get_char_dimension()
#the idea is 10kb is treated as 800 pixels
ratio = im_10kb_length/10000.0
im_seq_length = int(ratio*seq_length)
seq_dimension = (im_seq_length, char_height)
seq_length_dimension = ((len(repr(seq_length))+3)*char_width, char_height)
seq_name_dimension = (max_seq_name_length*char_width, char_height)
x_offset0 = 0
x_offset1 = x_offset0 + padding_width #seq starts
x_offset2 = x_offset1 + seq_dimension[0] # seq ends
x_offset3 = x_offset2 + padding_width #seq_length starts
x_offset4 = x_offset3 + seq_length_dimension[0] #seq_length ends
x_offset5 = x_offset4 + padding_width #seq_name starts
x_offset6 = x_offset5 + seq_name_dimension[0] #seq_name ends
y_offset0 = 0
y_offset1 = y_offset0 + padding_height #the row starts
y_offset2 = y_offset1 + seq_dimension[1] #the row ends
whole_dimension = (x_offset6 + padding_width, y_offset2 + padding_height)
#1st draw the seq line,
seq_im = Image.new('RGB', seq_dimension, (255, 255, 255))
seq_draw = ImageDraw.Draw(seq_im)
#draw the seq baseline in the middle
seq_draw.rectangle((0, seq_dimension[1]/2, seq_dimension[0], seq_dimension[1]/2+1), fill=(0,0,0))
for tf_info_row in tf_info_list:
tf_name, bs_strand, bs_disp_start, bs_disp_end = tf_info_row
im_bs_disp_start = int(ratio*bs_disp_start)
seq_draw.rectangle((im_bs_disp_start, 0, im_bs_disp_start+bs_width, seq_dimension[1]), fill=tf_name2color[tf_name])
if seq_strand == '-': #to rotate 180 if seq_strand == '-'
seq_im = seq_im.rotate(180)
box = (0,0,seq_dimension[0], seq_dimension[1])
seq_reg = seq_im.crop(box)
#2nd paste seq line into main image
im = Image.new('RGB',(whole_dimension[0],whole_dimension[1]),(255,255,255))
draw = ImageDraw.Draw(im)
box = (x_offset1, y_offset1, x_offset2, y_offset2)
im.paste(seq_reg, box)
#3rd draw seq_length
text_region = get_text_region(str(seq_length)+'(%s)'%seq_strand, seq_length_dimension, rotate=0) #no rotate
box = (x_offset3, y_offset1, x_offset4, y_offset2)
im.paste(text_region, box)
#4gh draw seq_name
seq_name = str(seq_name)
if len(seq_name)>max_seq_name_length:
seq_name = seq_name[:max_seq_name_length]
text_region = get_text_region(seq_name, seq_name_dimension, rotate=0) #no rotate
box = (x_offset5, y_offset1, x_offset6, y_offset2)
im.paste(text_region, box)
sys.stderr.write(".\n")
return im
def draw_tf_map(self, recurrence_rec_array_bs_no_list, no_of_datasets, mt_no2tf_name, \
output_fname, function_name_length, char_dimension, font):
"""
11-28-05 add grid
2006-12-13 add font
"""
sys.stderr.write("Drawing tf_map...\n")
no_of_tfs = len(recurrence_rec_array_bs_no_list)
char_width, char_height = char_dimension
dataset_no_length = len(repr(no_of_datasets))
dataset_no_dimension = (char_width*dataset_no_length, char_height)
#one is not rotated(dataset_no), one is rotated(recurrence)
function_name_dimension = (char_width*function_name_length, char_height) #will rotate
x_offset0 = 0
x_offset1 = dataset_no_dimension[0]
y_offset0 = 0
y_offset1 = function_name_dimension[0]
y_offset2 = y_offset1 + no_of_datasets*dataset_no_dimension[1]
y_offset3 = y_offset2 + dataset_no_dimension[0]
whole_dimension = (x_offset1+no_of_tfs*char_height, y_offset3)
im = Image.new('RGB',(whole_dimension[0],whole_dimension[1]),(255,255,255))
draw = ImageDraw.Draw(im)
#dataset_no section
for i in range(no_of_datasets):
text_region = get_text_region(repr(i+1), dataset_no_dimension, rotate=0, font=font) #no rotate
box = (x_offset0, y_offset1+i*dataset_no_dimension[1], x_offset1, y_offset1+(i+1)*dataset_no_dimension[1])
im.paste(text_region, box)
for i in range(len(recurrence_rec_array_bs_no_list)):
recurrence, recurrence_array, bs_no = recurrence_rec_array_bs_no_list[i]
x_offset_left = x_offset1+i*function_name_dimension[1]
x_offset_right = x_offset1+(i+1)*function_name_dimension[1]
#function_name
tf_name = '%s %s'%(bs_no, mt_no2tf_name[bs_no])
if len(tf_name)>function_name_length:
tf_name = tf_name[:function_name_length]
text_region = get_text_region(tf_name, function_name_dimension, font=font) #rotate
box = (x_offset_left, y_offset0, x_offset_right, y_offset1)
im.paste(text_region, box)
#fill in a cell for each dataset_no
for dataset_no in recurrence_array:
draw.rectangle((x_offset_left, y_offset1+(dataset_no-1)*dataset_no_dimension[1], \
x_offset_right, y_offset1+dataset_no*dataset_no_dimension[1]), fill=(0,255,0))
# write down the recurrence
text_region = get_text_region(repr(recurrence), dataset_no_dimension, font=font) #rotate
box = (x_offset_left, y_offset2, x_offset_right, y_offset3)
im.paste(text_region, box)
#11-28-05
draw_grid(im, draw, [x_offset1, y_offset1, whole_dimension[0], y_offset2], char_height, char_height)
im = im.rotate(270)
im.save(output_fname)
del im
sys.stderr.write("End drawing tf_map.\n")
def draw_tf_legend(self, tf_name_list, padding_width=5, max_tf_name_length = 20):
sys.stderr.write("Drawing tf_legend")
#transform tf_name_list into a distinct list
tf_name_set = Set(tf_name_list)
tf_name_list = list(tf_name_set)
tf_name_list.sort()
#how many cuts for 0 to 255 (no_of_partitions-1)^3 <= len(tf_name_list) <= no_of_partitions^3
no_of_partitions = int(math.ceil(math.pow(len(tf_name_list), 1/3.0)))
step = 256/no_of_partitions
#RGB three channels
color_list = []
for i in range(no_of_partitions):
for j in range(no_of_partitions):
for k in range(no_of_partitions):
color_list.append((step*i, step*j, step*k))
char_width, char_height = get_char_dimension()
tf_name_dimension = (char_width*max_tf_name_length, char_height)
legend_dimension = (5, char_height)
x_offset0 = 0
x_offset1 = x_offset0 + padding_width #tf_name begin
x_offset2 = x_offset1 + tf_name_dimension[0] #tf_name end
x_offset3 = x_offset2 + padding_width #legend begin
x_offset4 = x_offset3 + legend_dimension[0] #legend end
whole_dimension = (x_offset4 + padding_width, char_height*2*len(tf_name_list))
tf_name2color = {}
im = Image.new('RGB',(whole_dimension[0],whole_dimension[1]),(255,255,255))
draw = ImageDraw.Draw(im)
for i in range(len(tf_name_list)):
tf_name = tf_name_list[i]
tf_name2color[tf_name] = color_list[i]
if len(tf_name) >max_tf_name_length:
tf_name = tf_name[:max_tf_name_length]
text_region = get_text_region(tf_name, tf_name_dimension, rotate=0) #no rotate
y_offset_upper = i*2*tf_name_dimension[1]
y_offset_bottom = (i*2+1)*tf_name_dimension[1]
box = (x_offset1, y_offset_upper, x_offset2, y_offset_bottom)
im.paste(text_region, box)
draw.rectangle((x_offset3, y_offset_upper, x_offset4, y_offset_bottom), fill=color_list[i])
sys.stderr.write(".\n")
return im, tf_name2color
def get_composite_and_individual_tf_line(self, composite_tf_im, tf_name2binding_sites, \
seq_name, seq_length, seq_strand, tf_name2color, padding_width,\
padding_height, max_seq_name_length, bs_width, im_10kb_length):
sys.stderr.write("Drawing composite_and_individual_tf_line\n")
char_width, char_height = get_char_dimension()
tf_name_dimension = (char_width*max_seq_name_length, char_height)
tf_line_dimension = composite_tf_im.size
x_offset0 = 0
x_offset1 = x_offset0 + padding_width #tf_name starts
x_offset2 = x_offset1 + tf_name_dimension[0] #tf_name ends
x_offset3 = x_offset2 + padding_width #tf_line starts
x_offset4 = x_offset3 + tf_line_dimension[0] #tf_line ends
whole_dimension = (x_offset4, (len(tf_name2binding_sites)+1)*tf_line_dimension[1])
im = Image.new('RGB',(whole_dimension[0],whole_dimension[1]),(255,255,255))
draw = ImageDraw.Draw(im)
#1st paste the composite_tf_im
box = (x_offset3, 0, x_offset4, tf_line_dimension[1])
im.paste(composite_tf_im, box)
counter = 0
tf_name_list = tf_name2binding_sites.keys()
tf_name_list.sort()
for tf_name in tf_name_list:
tf_info_list = tf_name2binding_sites[tf_name]
counter += 1 #starting from 1 because composite_tf_im is 0
if len(tf_name) >max_seq_name_length:
tf_name = tf_name[:max_seq_name_length]
text_region = get_text_region(tf_name, tf_name_dimension, rotate=0) #no rotate
y_offset_upper = counter*tf_line_dimension[1]
y_offset_bottom = (counter+1)*tf_line_dimension[1]
box = (x_offset1, y_offset_upper+padding_height, x_offset2, y_offset_bottom-padding_height)
im.paste(text_region, box)
tf_line_im = self.draw_tf_line(seq_name, seq_length, seq_strand, tf_info_list, tf_name2color, \
padding_width, padding_height, max_seq_name_length, bs_width, im_10kb_length)
box = (x_offset3, y_offset_upper, x_offset4, y_offset_bottom)
im.paste(tf_line_im, box)
sys.stderr.write(".\n")
return im
def draw_function_map(self, recurrence_go_no_rec_array_cluster_id_ls, no_of_datasets, go_no2name, \
output_fname, function_name_length, char_dimension, no_of_functions, font):
"""
10-31-05 from misc.py. make it independent and return something for draw_gene_function_map()
11-28-05 add grid
11-28-05 include go_no in go_name
2006-12-13 add font
"""
sys.stderr.write("Drawing function_map...\n")
char_width, char_height = char_dimension
dataset_no_length = len(repr(no_of_datasets))
dataset_no_dimension = (char_width*dataset_no_length, char_height) #one is not rotated, one is rotated
no_of_clusters_dimension = (char_width*7, char_height) #will rotate
function_name_dimension = (char_width*function_name_length, char_height) #will rotate
x_offset0 = 0
x_offset1 = dataset_no_dimension[0]
y_offset0 = 0
y_offset1 = function_name_dimension[0]
y_offset2 = y_offset1 + no_of_datasets*dataset_no_dimension[1]
y_offset3 = y_offset2 + dataset_no_dimension[0]
whole_dimension = (x_offset1+no_of_functions*char_height, \
y_offset3+no_of_clusters_dimension[0])
im = Image.new('RGB',(whole_dimension[0],whole_dimension[1]),(255,255,255))
draw = ImageDraw.Draw(im)
#dataset_no section
for i in range(no_of_datasets):
text_region = get_text_region(repr(i+1), dataset_no_dimension, rotate=0, font=font) #no rotate
box = (x_offset0, y_offset1+i*dataset_no_dimension[1], x_offset1, y_offset1+(i+1)*dataset_no_dimension[1])
im.paste(text_region, box)
#10-31-05 following for draw_gene_function_map() to ensure correspondence.
go_no2index = {}
function_name_box = (x_offset1,y_offset0, whole_dimension[0], y_offset1)
for i in range(len(recurrence_go_no_rec_array_cluster_id_ls)):
recurrence, go_no, recurrence_array, mcl_id_set = recurrence_go_no_rec_array_cluster_id_ls[i]
go_no2index[go_no] = i #10-31-05
x_offset_left = x_offset1+i*function_name_dimension[1]
x_offset_right = x_offset1+(i+1)*function_name_dimension[1]
#function_name
go_name = '%s %s'%(go_no, go_no2name[go_no]) #11-28-05 include go_no
if len(go_name)>function_name_length:
go_name = go_name[:function_name_length]
text_region = get_text_region(go_name, function_name_dimension, font=font) #rotate
box = (x_offset_left, y_offset0, x_offset_right, y_offset1)
im.paste(text_region, box)
#fill in a cell for each dataset_no
for dataset_no in recurrence_array:
draw.rectangle((x_offset_left, y_offset1+(dataset_no-1)*dataset_no_dimension[1], \
x_offset_right, y_offset1+dataset_no*dataset_no_dimension[1]), fill=(0,255,0))
# write down the recurrence
text_region = get_text_region(repr(recurrence), dataset_no_dimension, font=font) #rotate
box = (x_offset_left, y_offset2, x_offset_right, y_offset3)
im.paste(text_region, box)
#write down the no_of_clusters
text_region = get_text_region(repr(len(mcl_id_set)), no_of_clusters_dimension, font=font) #rotate
box = (x_offset_left, y_offset3, x_offset_right, whole_dimension[1])
im.paste(text_region, box)
function_name_region = im.crop(function_name_box) #10-31-05
#11-28-05
draw_grid(im, draw, [x_offset1, y_offset1, whole_dimension[0], y_offset2], char_height, char_height)
im = im.rotate(270)
im.save(output_fname)
del im
sys.stderr.write("End drawing function_map.\n")
return go_no2index, function_name_region
