/
alldata_visualizer.py
269 lines (238 loc) · 14.1 KB
/
alldata_visualizer.py
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import numpy as np
import pandas as pd
import argparse
import sys
from bokeh import events
from bokeh.io import save, export_svgs
from bokeh.resources import CDN
from bokeh.embed import components, file_html
from bokeh.palettes import brewer
from bokeh.plotting import figure, show, output_file
from bokeh.models import ColumnDataSource, LabelSet, ColorBar, BasicTicker, PrintfTickFormatter,HoverTool, LinearColorMapper, Slider, CustomJS, Label, WheelZoomTool, ResetTool, Button, TextInput
from bokeh.models.widgets import Panel, Paragraph, Div
from bokeh.layouts import gridplot, column, layout, widgetbox, row
from bokeh.transform import transform
import subprocess
import os
color_palette=[
'#5e4fa2', '#3288bd', '#66c2a5', '#abdda4', '#e6f598', '#ffffbf', '#fee08b', '#fdae61',
'#f46d43', '#d53e4f', '#9e0142',
'#003366', '#dec9ab', '#d25757', '#f7d708','#1c29b5', '#b0c997', '#005555', '#f9c3d3', '#0f4c81',
'#edc06a', '#bd5915', '#b097c9', '#c2002c', '#808080',
'#66c2a5', '#fc8d62', '#8da0cb', '#e78ac3', '#a6d854', '#ffd92f', '#e5c494', '#b3b3b3',
'#1b9e77', '#d95f02', '#7570b3', '#e7298a', '#66a61e', '#e6ab02', '#a6761d', '#666666',
'#8dd3c7', '#ffffb3', '#bebada', '#fb8072', '#80b1d3', '#fdb462', '#b3de69', '#fccde5',
'#d9d9d9','#bc80bd', '#ccebc5', '#ffed6f',
'#bc9797', '#a0db8e', '#d69ce1', '#caffcd', '#ffcaf8', '#cafff7', '#f1b4b2', '#030449',
'#feff97', '#fd81eb', '#8fb8ff', '#bdffa3', '#ffb5b5', '#0f4c81', '#d7d8ee','#73c7de','#aaaacc',
'#758eb7', '#f2b6ae', '#f0a890', '#a860a8', '#604890', '#f07878', '#443133', '#ffdecc', '#65bfc1',
'#ffad19', '#ff9e7d', '#dda97b','#a1b1cc','#d6a562','#c9a48f','#c7906d','#f9733e',
'#ffc104', '#624a4c', '#c1b8c9',
"#FFFF00", "#1CE6FF", "#FF34FF", "#FF4A46", "#008941", "#006FA6", "#A30059",
"#FFDBE5", "#7A4900", "#0000A6", "#63FFAC", "#B79762", "#004D43", "#8FB0FF", "#997D87",
"#5A0007", "#809693", "#FEFFE6", "#1B4400", "#4FC601", "#3B5DFF", "#4A3B53", "#FF2F80",
"#61615A", "#BA0900", "#6B7900", "#00C2A0", "#FFAA92", "#FF90C9", "#B903AA", "#D16100",
"#DDEFFF", "#000035", "#7B4F4B", "#A1C299", "#300018", "#0AA6D8", "#013349", "#00846F",
"#372101", "#FFB500", "#C2FFED", "#A079BF", "#CC0744", "#C0B9B2", "#C2FF99", "#001E09",
"#00489C", "#6F0062", "#0CBD66", "#EEC3FF", "#456D75", "#B77B68", "#7A87A1", "#788D66",
"#885578", "#FAD09F", "#FF8A9A", "#D157A0", "#BEC459", "#456648", "#0086ED", "#886F4C",
"#34362D", "#B4A8BD", "#00A6AA", "#452C2C", "#636375", "#A3C8C9", "#FF913F", "#938A81",
"#575329", "#00FECF", "#B05B6F", "#8CD0FF", "#3B9700", "#04F757", "#C8A1A1", "#1E6E00",
"#7900D7", "#A77500", "#6367A9", "#A05837", "#6B002C", "#772600", "#D790FF", "#9B9700",
"#549E79", "#FFF69F", "#201625", "#72418F", "#BC23FF", "#99ADC0", "#3A2465", "#922329",
"#5B4534", "#FDE8DC", "#404E55", "#0089A3", "#CB7E98", "#A4E804", "#324E72", "#6A3A4C",
"#83AB58", "#001C1E", "#D1F7CE", "#004B28", "#C8D0F6", "#A3A489", "#806C66", "#222800",
"#BF5650", "#E83000", "#66796D", "#DA007C", "#FF1A59", "#8ADBB4", "#1E0200", "#5B4E51",
"#C895C5", "#320033", "#FF6832", "#66E1D3", "#CFCDAC", "#D0AC94", "#7ED379", "#012C58",
"#7A7BFF", "#D68E01", "#353339", "#78AFA1", "#FEB2C6", "#75797C", "#837393", "#943A4D",
"#B5F4FF", "#D2DCD5", "#9556BD", "#6A714A", "#001325", "#02525F", "#0AA3F7", "#E98176",
"#DBD5DD", "#5EBCD1", "#3D4F44", "#7E6405", "#02684E", "#962B75", "#8D8546", "#9695C5",
"#E773CE", "#D86A78", "#3E89BE", "#CA834E", "#518A87", "#5B113C", "#55813B", "#E704C4",
"#00005F", "#A97399", "#4B8160", "#59738A", "#FF5DA7", "#F7C9BF", "#643127", "#513A01",
"#6B94AA", "#51A058", "#A45B02", "#1D1702", "#E20027", "#E7AB63", "#4C6001", "#9C6966",
"#64547B", "#97979E", "#006A66", "#391406", "#F4D749", "#0045D2", "#006C31", "#DDB6D0",
"#7C6571", "#9FB2A4", "#00D891", "#15A08A", "#BC65E9", "#FFFFFE", "#C6DC99", "#203B3C",
"#671190", "#6B3A64", "#F5E1FF", "#FFA0F2", "#CCAA35", "#374527", "#8BB400", "#797868",
"#C6005A", "#3B000A", "#C86240", "#29607C", "#402334", "#7D5A44", "#CCB87C", "#B88183",
"#AA5199", "#B5D6C3", "#A38469", "#9F94F0", "#A74571", "#B894A6", "#71BB8C", "#00B433",
"#789EC9", "#6D80BA", "#953F00", "#5EFF03", "#E4FFFC", "#1BE177", "#BCB1E5", "#76912F",
"#003109", "#0060CD", "#D20096", "#895563", "#29201D", "#5B3213", "#A76F42", "#89412E",
"#1A3A2A", "#494B5A", "#A88C85", "#F4ABAA", "#A3F3AB", "#00C6C8", "#EA8B66", "#958A9F",
"#BDC9D2", "#9FA064", "#BE4700", "#658188", "#83A485", "#453C23", "#47675D", "#3A3F00",
"#061203", "#DFFB71", "#868E7E", "#98D058", "#6C8F7D", "#D7BFC2", "#3C3E6E", "#D83D66",
"#2F5D9B", "#6C5E46", "#D25B88", "#5B656C", "#00B57F", "#545C46", "#866097", "#365D25",
"#252F99", "#00CCFF", "#674E60", "#FC009C", "#92896B",
'#5e4fa2', '#3288bd', '#66c2a5', '#abdda4', '#e6f598', '#ffffbf', '#fee08b', '#fdae61',
'#f46d43', '#d53e4f', '#9e0142',
'#8dd3c7', '#ffffb3', '#bebada', '#fb8072', '#80b1d3', '#fdb462', '#b3de69', '#fccde5',
'#d9d9d9','#bc80bd', '#ccebc5', '#ffed6f',
'#66c2a5', '#fc8d62', '#8da0cb', '#e78ac3', '#a6d854', '#ffd92f', '#e5c494', '#b3b3b3',
'#1b9e77', '#d95f02', '#7570b3', '#e7298a', '#66a61e', '#e6ab02', '#a6761d', '#666666',
'#bc9797', '#a0db8e', '#d69ce1', '#caffcd', '#ffcaf8', '#cafff7', '#f1b4b2', '#030449',
'#003366', '#dec9ab', '#d25757', '#f7d708','#1c29b5', '#b0c997', '#005555', '#f9c3d3', '#0f4c81',
'#edc06a', '#bd5915', '#b097c9', '#c2002c', '#808080',
'#feff97', '#fd81eb', '#8fb8ff', '#bdffa3', '#ffb5b5', '#0f4c81', '#d7d8ee','#73c7de','#aaaacc',
'#758eb7', '#f2b6ae', '#f0a890', '#a860a8', '#604890', '#f07878', '#443133', '#ffdecc', '#65bfc1',
'#ffad19', '#ff9e7d', '#dda97b','#a1b1cc','#d6a562','#c9a48f','#c7906d','#f9733e',
'#ffc104', '#624a4c', '#c1b8c9',
"#FFFF00", "#1CE6FF", "#FF34FF", "#FF4A46", "#008941", "#006FA6", "#A30059",
"#FFDBE5", "#7A4900", "#0000A6", "#63FFAC", "#B79762", "#004D43", "#8FB0FF", "#997D87",
"#5A0007", "#809693", "#FEFFE6", "#1B4400", "#4FC601", "#3B5DFF", "#4A3B53", "#FF2F80",
"#61615A", "#BA0900", "#6B7900", "#00C2A0", "#FFAA92", "#FF90C9", "#B903AA", "#D16100",
"#DDEFFF", "#000035", "#7B4F4B", "#A1C299", "#300018", "#0AA6D8", "#013349", "#00846F",
"#372101", "#FFB500", "#C2FFED", "#A079BF", "#CC0744", "#C0B9B2", "#C2FF99", "#001E09",
"#00489C", "#6F0062", "#0CBD66", "#EEC3FF", "#456D75", "#B77B68", "#7A87A1", "#788D66",
"#885578", "#FAD09F", "#FF8A9A", "#D157A0", "#BEC459", "#456648", "#0086ED", "#886F4C",
"#34362D", "#B4A8BD", "#00A6AA", "#452C2C", "#636375", "#A3C8C9", "#FF913F", "#938A81",
"#575329", "#00FECF", "#B05B6F", "#8CD0FF", "#3B9700", "#04F757", "#C8A1A1", "#1E6E00",
"#7900D7", "#A77500", "#6367A9", "#A05837", "#6B002C", "#772600", "#D790FF", "#9B9700",
"#549E79", "#FFF69F", "#201625", "#72418F", "#BC23FF", "#99ADC0", "#3A2465", "#922329",
"#5B4534", "#FDE8DC", "#404E55", "#0089A3", "#CB7E98", "#A4E804", "#324E72", "#6A3A4C",
"#83AB58", "#001C1E", "#D1F7CE", "#004B28", "#C8D0F6", "#A3A489", "#806C66", "#222800",
"#BF5650", "#E83000", "#66796D", "#DA007C", "#FF1A59", "#8ADBB4", "#1E0200", "#5B4E51",
"#C895C5", "#320033", "#FF6832", "#66E1D3", "#CFCDAC", "#D0AC94", "#7ED379", "#012C58",
"#7A7BFF", "#D68E01", "#353339", "#78AFA1", "#FEB2C6", "#75797C", "#837393", "#943A4D",
"#B5F4FF", "#D2DCD5", "#9556BD", "#6A714A", "#001325", "#02525F", "#0AA3F7", "#E98176",
"#DBD5DD", "#5EBCD1", "#3D4F44", "#7E6405", "#02684E", "#962B75", "#8D8546", "#9695C5",
"#E773CE", "#D86A78", "#3E89BE", "#CA834E", "#518A87", "#5B113C", "#55813B", "#E704C4",
"#00005F", "#A97399", "#4B8160", "#59738A", "#FF5DA7", "#F7C9BF", "#643127", "#513A01",
"#6B94AA", "#51A058", "#A45B02", "#1D1702", "#E20027", "#E7AB63", "#4C6001", "#9C6966",
"#64547B", "#97979E", "#006A66", "#391406", "#F4D749", "#0045D2", "#006C31", "#DDB6D0",
"#7C6571", "#9FB2A4", "#00D891", "#15A08A", "#BC65E9", "#FFFFFE", "#C6DC99", "#203B3C",
"#671190", "#6B3A64", "#F5E1FF", "#FFA0F2", "#CCAA35", "#374527", "#8BB400", "#797868",
"#C6005A", "#3B000A", "#C86240", "#29607C", "#402334", "#7D5A44", "#CCB87C", "#B88183",
"#AA5199", "#B5D6C3", "#A38469", "#9F94F0", "#A74571", "#B894A6", "#71BB8C", "#00B433",
"#789EC9", "#6D80BA", "#953F00", "#5EFF03", "#E4FFFC", "#1BE177", "#BCB1E5", "#76912F",
"#003109", "#0060CD", "#D20096", "#895563", "#29201D", "#5B3213", "#A76F42", "#89412E",
"#1A3A2A", "#494B5A", "#A88C85", "#F4ABAA", "#A3F3AB", "#00C6C8", "#EA8B66", "#958A9F",
"#BDC9D2", "#9FA064", "#BE4700", "#658188", "#83A485", "#453C23", "#47675D", "#3A3F00",
"#061203", "#DFFB71", "#868E7E", "#98D058", "#6C8F7D", "#D7BFC2", "#3C3E6E", "#D83D66",
"#2F5D9B", "#6C5E46", "#D25B88", "#5B656C", "#00B57F", "#545C46", "#866097", "#365D25",
"#252F99", "#00CCFF", "#674E60", "#FC009C", "#92896B"
]
def configure_plot(fig, sample_list, sample_xaxis):
fig.xaxis.major_label_overrides = dict(zip(sample_xaxis, sample_list))
fig.xaxis.minor_tick_line_color = None
fig.title.text_font_size = "20pt"
fig.xaxis.major_label_text_font_size = '16pt'
fig.yaxis.major_label_text_font_size = '16pt'
fig.yaxis.axis_label = "Relative Frequency"
fig.yaxis.axis_label_text_font_size = '18pt'
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Syph visualizer for all data')
parser.add_argument('alldata_filtered', help='alldata_filtered.csv data table from tprk_pipeline.py')
parser.add_argument('metadata', help='metadata.csv, same as used with tprk_pipeline.py')
parser.add_argument('-svg', action='store_true', help='Use this flag to output graphs in .svg format. '
'By default, plots will be in .html.')
try:
args = parser.parse_args()
except:
parser.print_help()
sys.exit(0)
df = pd.read_csv(args.alldata_filtered,index_col=False)
metadata_file = args.metadata
source = ColumnDataSource(df)
# Get list of sample names from metadata file and make xaxis spots for all of them.
sample_list = []
sample_xaxis = []
read_metadata_file = open(metadata_file, "r")
metadata_file_lines = read_metadata_file.readlines()
for paired_samples in metadata_file_lines:
sample, illumina_sample, pacbio_sample = paired_samples.split(",")
if(sample!="SampleName"):
sample_list.append(sample)
sample_xaxis.append(len(sample_list)*10)
variable_regions_list = ['V1','V2','V3','V4','V5','V6','V7']
variable_region_figs = []
variable_region_hms = []
df_columns = list(df)
sample_list.sort()
# Drop PacBio columns
for column in df_columns:
if "PB_" in column or "Count" in column:
df = df.drop(labels=column, axis=1)
df_columns = list(df)
# Replace NaNs with 0s
df.fillna(0, inplace=True)
# Initialize palettes
blues = brewer['Blues'][9][0:7]
bugn = brewer['BuGn'][9][0:7]
bupu = brewer['Purples'][8][0:7]
orrd = brewer['OrRd'][9][0:7]
gnbu = brewer['GnBu'][9][0:7]
purd = brewer['PuRd'][9][0:7]
ylgn = brewer['YlGn'][9][0:7]
for variable_region in variable_regions_list:
region_df = df.loc[df.Region==variable_region]
region_df = region_df.drop(labels="Region", axis=1)
color_num = 0
sample_reads = []
hm_x = []
hm_y = []
hm_values = []
hm_yaxis = []
data = {'samples': sample_list}
for index, row in region_df.iterrows():
read_seq = row[0]
sample_frequencies = []
num = 0
row_parts_all_zero = True
for i, row_parts in enumerate(row):
if(i!=0):
num = float(row_parts)
if(float(num)!=0):
row_parts_all_zero = False
hm_x.append(sample_list[i-1])
hm_y.append(read_seq)
hm_values.append(num)
sample_frequencies.append(num)
# Only use rows with actual data in it
if not row_parts_all_zero and read_seq!="":
sample_reads.append(read_seq)
data[read_seq] = sample_frequencies
color_num = color_num + 1
df2 = pd.DataFrame()
df2['x']=hm_x
df2['y']=hm_y
df2['values']=hm_values
source = ColumnDataSource(df2)
if(variable_region=="V1"):
brew_pal = blues
elif(variable_region=="V2"):
brew_pal = bugn
elif(variable_region=="V3"):
brew_pal = bupu
elif(variable_region=="V4"):
brew_pal = orrd
elif(variable_region=="V5"):
brew_pal = gnbu
elif(variable_region=="V6"):
brew_pal = ylgn
else:
brew_pal = purd
# Reverse the colors so darker colors at max
brew_pal = brew_pal[::-1]
mapper = LinearColorMapper(palette=brew_pal, low=0.1, high=100, nan_color = "#d3d3d3")
hm = figure(x_range=sample_list, y_range=sample_reads, title = variable_region,
toolbar_location = None, x_axis_location = "above", #background_fill_color = "#d3d3d3",
plot_height = (len(sample_reads)*20),
# plot_width = (len(sample_list)*25) + (len(max(sample_reads, key = len)) * 8),
min_border_right = 80,
y_axis_location = "left",
tooltips=[('Read','@y'),('Strain','@x'),('Frequency','@values')])
hm.rect(x='x', y='y', width = 1, height =1, source=source,
line_color=None, fill_color=transform('values', mapper), hover_line_color = 'black',
hover_color = transform('values',mapper))
color_bar = ColorBar(color_mapper = mapper, major_label_text_font_size="5pt",
ticker=BasicTicker(desired_num_ticks=len(purd)),
formatter=PrintfTickFormatter(format="%d%%"),
label_standoff=6, border_line_color=None, location=(0, 0))
hm.add_layout(color_bar, 'right')
hm.xaxis.major_label_orientation = 1.0
hm.grid.grid_line_color = None
hm.axis.axis_line_color = None
hm.axis.major_tick_line_color = None
variable_region_hms.append(hm)
grid2 = gridplot(variable_region_hms,ncols=1)
output_file("all_heatmap.html", title = "Heatmap")
save(grid2, sizing_mode = "scale_width")