maplot: maplot.py annotate

annotate maplot.py @ 0:835867b8ebd9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab

author	iuc
date	Thu, 15 May 2025 12:55:02 +0000
parents
children

rev	line source
0 835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	1 import argparse
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	2 from typing import Dict, List, Tuple
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	3
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	4 import matplotlib.pyplot as plt
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	5 import numpy as np
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	6 import pandas as pd
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	7 import plotly.graph_objects as go
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	8 import plotly.io as pio
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	9 import plotly.subplots as sp
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	10 import statsmodels.api as sm # to build a LOWESS model
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	11 from scipy.stats import gaussian_kde
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	12
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	13
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	14 # subplot titles
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	15 def make_subplot_titles(sample_names: List[str]) -> List[str]:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	16 """Generates subplot titles for the MA plot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	17
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	18 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	19 sample_names (list): List of sample names.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	20
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	21 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	22 list: List of subplot titles.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	23 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	24 subplot_titles = []
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	25 num_samples = len(sample_names)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	26 for i in range(num_samples):
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	27 for j in range(num_samples):
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	28 if i == j:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	29 subplot_titles.append(f"{sample_names[i]}")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	30 else:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	31 subplot_titles.append(f"{sample_names[i]} vs. {sample_names[j]}")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	32 return subplot_titles
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	33
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	34
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	35 def densities(x: np.ndarray, y: np.ndarray) -> np.ndarray:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	36 """Calculates the density of points for a scatter plot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	37
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	38 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	39 x (array-like): X-axis values.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	40 y (array-like): Y-axis values.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	41
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	42 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	43 array: Density values for the points.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	44 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	45 values = np.vstack([x, y])
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	46 return gaussian_kde(values)(values)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	47
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	48
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	49 def movingaverage(data: np.ndarray, window_width: int) -> np.ndarray:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	50 """Calculates the moving average of the data.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	51
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	52 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	53 data (array-like): Input data.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	54 window_width (int): Width of the moving window.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	55
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	56 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	57 array: Moving average values.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	58 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	59 cumsum_vec = np.cumsum(np.insert(data, 0, 0))
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	60 ma_vec = (cumsum_vec[window_width:] - cumsum_vec[:-window_width]) / window_width
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	61 return ma_vec
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	62
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	63
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	64 def update_max(current: float, values: np.ndarray) -> float:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	65 """Updates the maximum value.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	66
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	67 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	68 current (float): Current maximum value.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	69 values (array-like): Array of values to compare.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	70
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	71 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	72 float: Updated maximum value.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	73 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	74 return max(current, np.max(values))
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	75
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	76
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	77 def get_indices(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	78 num_samples: int, num_cols: int, plot_num: int
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	79 ) -> Tuple[int, int, int, int]:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	80 """Calculates the indices for subplot placement.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	81
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	82 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	83 num_samples (int): Number of samples.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	84 num_cols (int): Number of columns in the subplot grid.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	85 plot_num (int): Plot number.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	86
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	87 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	88 tuple: Indices for subplot placement (i, j, col, row).
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	89 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	90 i = plot_num // num_samples
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	91 j = plot_num % num_samples
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	92 col = plot_num % num_cols + 1
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	93 row = plot_num // num_cols + 1
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	94 return i, j, col, row
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	95
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	96
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	97 def create_subplot_data(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	98 frac: float,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	99 it: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	100 num_bins: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	101 window_width: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	102 samples: pd.DataFrame,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	103 i: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	104 j: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	105 ) -> Dict:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	106 """Creates data for a single subplot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	107
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	108 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	109 frac (float): LOESS smoothing parameter.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	110 it (int): Number of iterations for LOESS smoothing.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	111 num_bins (int): Number of bins for histogram.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	112 window_width (int): Window width for moving average.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	113 samples (DataFrame): DataFrame containing sample data.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	114 i (int): Index of the first sample.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	115 j (int): Index of the second sample.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	116
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	117 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	118 dict: Data for the subplot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	119 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	120 subplot_data = {}
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	121 subplot_data["mean"] = np.log(samples.iloc[:, [i, j]].mean(axis=1))
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	122 if i == j:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	123 counts, bins = np.histogram(subplot_data["mean"], bins=num_bins)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	124 subplot_data["bins"] = bins
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	125 subplot_data["counts"] = counts
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	126 subplot_data["counts_smoothed"] = movingaverage(counts, window_width)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	127 subplot_data["max_counts"] = np.max(counts)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	128 else:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	129 subplot_data["log_fold_change"] = np.log2(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	130 samples.iloc[:, i] / samples.iloc[:, j]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	131 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	132 subplot_data["max_log_fold_change"] = np.max(subplot_data["log_fold_change"])
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	133 subplot_data["densities"] = densities(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	134 subplot_data["mean"], subplot_data["log_fold_change"]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	135 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	136 subplot_data["regression"] = sm.nonparametric.lowess(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	137 subplot_data["log_fold_change"], subplot_data["mean"], frac=frac, it=it
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	138 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	139 return subplot_data
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	140
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	141
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	142 def create_plot_data(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	143 frac: float,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	144 it: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	145 num_bins: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	146 window_width: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	147 samples: pd.DataFrame,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	148 num_samples: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	149 num_plots: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	150 num_cols: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	151 ) -> List[Dict]:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	152 """Creates data for all subplots.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	153
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	154 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	155 frac (float): LOESS smoothing parameter.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	156 it (int): Number of iterations for LOESS smoothing.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	157 num_bins (int): Number of bins for histogram.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	158 window_width (int): Window width for moving average.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	159 samples (DataFrame): DataFrame containing sample data.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	160 num_samples (int): Number of samples.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	161 num_plots (int): Number of plots.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	162 num_cols (int): Number of columns in the subplot grid.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	163
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	164 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	165 list: List of data for each subplot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	166 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	167 plots_data = []
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	168 for plot_num in range(num_plots):
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	169 i, j, _, _ = get_indices(num_samples, num_cols, plot_num)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	170 subplot_data = create_subplot_data(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	171 frac, it, num_bins, window_width, samples, i, j
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	172 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	173 plots_data.append(subplot_data)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	174 return plots_data
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	175
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	176
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	177 def ma_plots_plotly(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	178 num_rows: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	179 num_cols: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	180 num_plots: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	181 plots_data: List[Dict],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	182 sample_names: List[str],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	183 size: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	184 ylim_hist: float,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	185 ylim_ma: float,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	186 features: np.ndarray,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	187 ) -> go.Figure:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	188 """Generates MA plots using Plotly.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	189
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	190 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	191 num_rows (int): Number of rows in the subplot grid.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	192 num_cols (int): Number of columns in the subplot grid.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	193 num_plots (int): Number of plots.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	194 plots_data (list): List of data for each subplot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	195 sample_names (list): List of sample names.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	196 size (int): Size of the plot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	197 ylim_hist (float): Y-axis limit for histograms.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	198 ylim_ma (float): Y-axis limit for MA plots.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	199 features (array-like): Feature names.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	200
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	201 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	202 Figure: Plotly figure object.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	203 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	204 fig = sp.make_subplots(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	205 rows=num_rows,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	206 cols=num_cols,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	207 shared_xaxes="all",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	208 subplot_titles=make_subplot_titles(sample_names),
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	209 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	210
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	211 for plot_num in range(num_plots):
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	212 i, j, col, row = get_indices(len(sample_names), num_cols, plot_num)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	213 subplot_data = plots_data[plot_num]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	214
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	215 mean = subplot_data["mean"]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	216
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	217 if i == j:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	218 # Plot histogram on the diagonal
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	219 hist_bar = go.Bar(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	220 x=subplot_data["bins"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	221 y=subplot_data["counts"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	222 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	223 fig.add_trace(hist_bar, row=row, col=col)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	224
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	225 hist_line = go.Scatter(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	226 x=subplot_data["bins"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	227 y=subplot_data["counts_smoothed"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	228 marker=dict(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	229 color="red",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	230 ),
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	231 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	232 fig.add_trace(hist_line, row=row, col=col)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	233 fig.update_yaxes(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	234 title_text="Counts",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	235 range=[0, ylim_hist],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	236 matches="y1",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	237 showticklabels=True,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	238 row=row,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	239 col=col,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	240 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	241 else:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	242 log_fold_change = subplot_data["log_fold_change"]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	243 scatter = go.Scatter(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	244 x=mean,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	245 y=log_fold_change,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	246 mode="markers",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	247 marker=dict(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	248 color=subplot_data["densities"], symbol="circle", colorscale="jet"
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	249 ),
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	250 name=f"{sample_names[i]} vs {sample_names[j]}",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	251 text=features,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	252 hovertemplate="<b>%{text}</b><br>Log Mean: %{x}<br>Log2 Fold Change: %{y}<extra></extra>",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	253 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	254 fig.add_trace(scatter, row=row, col=col)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	255
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	256 regression = subplot_data["regression"]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	257 line = go.Scatter(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	258 x=regression[:, 0],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	259 y=regression[:, 1],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	260 mode="lines",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	261 line=dict(color="red"),
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	262 name=f"LOWESS {sample_names[i]} vs. {sample_names[j]}",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	263 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	264 fig.add_trace(line, row=row, col=col)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	265
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	266 fig.update_yaxes(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	267 title_text="Log2 Fold Change",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	268 range=[-ylim_ma, ylim_ma],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	269 matches="y2",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	270 showticklabels=True,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	271 row=row,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	272 col=col,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	273 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	274 fig.update_xaxes(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	275 title_text="Log Mean Intensity", showticklabels=True, row=row, col=col
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	276 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	277
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	278 # Update layout for the entire figure
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	279 fig.update_layout(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	280 height=size * num_rows,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	281 width=size * num_cols,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	282 showlegend=False,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	283 template="simple_white", # Apply the 'plotly_white' template
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	284 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	285 return fig
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	286
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	287
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	288 def ma_plots_matplotlib(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	289 num_rows: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	290 num_cols: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	291 num_plots: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	292 pots_data: List[Dict],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	293 sample_names: List[str],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	294 size: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	295 ylim_hist: float,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	296 ylim_ma: float,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	297 window_width: int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	298 ) -> plt.Figure:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	299 """Generates MA plots using Matplotlib.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	300
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	301 Args:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	302 num_rows (int): Number of rows in the subplot grid.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	303 num_cols (int): Number of columns in the subplot grid.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	304 num_plots (int): Number of plots.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	305 pots_data (list): List of data for each subplot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	306 sample_names (list): List of sample names.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	307 size (int): Size of the plot.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	308 ylim_hist (float): Y-axis limit for histograms.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	309 ylim_ma (float): Y-axis limit for MA plots.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	310 window_width (int): Window width for moving average.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	311
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	312 Returns:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	313 Figure: Matplotlib figure object.
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	314 """
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	315 subplot_titles = make_subplot_titles(sample_names)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	316 fig, axes = plt.subplots(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	317 num_rows,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	318 num_cols,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	319 figsize=(size * num_cols / 100, size * num_rows / 100),
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	320 dpi=300,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	321 sharex="all",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	322 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	323 axes = axes.flatten()
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	324
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	325 for plot_num in range(num_plots):
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	326 i, j, _, _ = get_indices(len(sample_names), num_cols, plot_num)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	327 subplot_data = pots_data[plot_num]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	328
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	329 mean = subplot_data["mean"]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	330
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	331 ax = axes[plot_num]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	332
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	333 if i == j:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	334 # Plot histogram on the diagonal
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	335 ax.bar(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	336 subplot_data["bins"][:-1],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	337 subplot_data["counts"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	338 width=np.diff(subplot_data["bins"]),
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	339 edgecolor="black",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	340 align="edge",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	341 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	342
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	343 # Plot moving average line
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	344 ax.plot(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	345 subplot_data["bins"][window_width // 2: -window_width // 2],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	346 subplot_data["counts_smoothed"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	347 color="red",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	348 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	349
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	350 ax.set_ylabel("Counts")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	351 ax.set_ylim(0, ylim_hist)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	352 else:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	353 # Scatter plot
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	354 ax.scatter(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	355 mean,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	356 subplot_data["log_fold_change"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	357 c=subplot_data["densities"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	358 cmap="jet",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	359 edgecolor="black",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	360 label=f"{sample_names[i]} vs {sample_names[j]}",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	361 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	362
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	363 # Regression line
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	364 regression = subplot_data["regression"]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	365 ax.plot(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	366 regression[:, 0],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	367 regression[:, 1],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	368 color="red",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	369 label=f"LOWESS {sample_names[i]} vs. {sample_names[j]}",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	370 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	371
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	372 ax.set_ylabel("Log2 Fold Change")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	373 ax.set_ylim(-ylim_ma, ylim_ma)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	374
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	375 ax.set_xlabel("Log Mean Intensity")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	376 ax.tick_params(labelbottom=True) # Force showing x-tick labels
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	377 ax.set_title(subplot_titles[plot_num]) # Add subplot title
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	378
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	379 # Adjust layout
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	380 plt.tight_layout()
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	381 return fig
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	382
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	383
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	384 def main():
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	385 """Main function to generate MA plots."""
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	386 parser = argparse.ArgumentParser(description="Generate MA plots.")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	387 parser.add_argument("--file_path", type=str, help="Path to the input CSV file")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	388 parser.add_argument("--file_extension", type=str, help="File extension")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	389 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	390 "--frac", type=float, default=4 / 5, help="LOESS smoothing parameter"
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	391 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	392 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	393 "--it", type=int, default=5, help="Number of iterations for LOESS smoothing"
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	394 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	395 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	396 "--num_bins", type=int, default=100, help="Number of bins for histogram"
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	397 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	398 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	399 "--window_width", type=int, default=5, help="Window width for moving average"
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	400 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	401 parser.add_argument("--size", type=int, default=500, help="Size of the plot")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	402 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	403 "--scale", type=int, default=3, help="Scale factor for the plot"
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	404 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	405 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	406 "--y_scale_factor", type=float, default=1.1, help="Y-axis scale factor"
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	407 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	408 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	409 "--max_num_cols",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	410 type=int,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	411 default=100,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	412 help="Maximum number of columns in the plot",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	413 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	414 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	415 "--interactive",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	416 action="store_true",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	417 help="Generate interactive plot using Plotly",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	418 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	419 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	420 "--output_format",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	421 type=str,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	422 default="pdf",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	423 choices=["pdf", "png", "html"],
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	424 help="Output format for the plot",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	425 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	426 parser.add_argument(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	427 "--output_file",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	428 type=str,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	429 default="ma_plot",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	430 help="Output file name without extension",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	431 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	432
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	433 args = parser.parse_args()
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	434
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	435 # Load the data
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	436 file_extension = args.file_extension.lower()
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	437 if file_extension == "csv":
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	438 data = pd.read_csv(args.file_path)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	439 elif file_extension in ["txt", "tsv", "tabular"]:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	440 data = pd.read_csv(args.file_path, sep="\t")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	441 elif file_extension == "parquet":
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	442 data = pd.read_parquet(args.file_path)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	443 else:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	444 raise ValueError(f"Unsupported file format: {file_extension}")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	445
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	446 features = data.iloc[:, 0] # Assuming the first column is the feature names
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	447 samples = data.iloc[:, 1:] # and the rest are samples
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	448
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	449 # Create a subplot figure
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	450 num_samples = samples.shape[1]
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	451 sample_names = samples.columns
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	452 num_plots = num_samples**2
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	453 num_cols = min(num_samples, args.max_num_cols)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	454 num_rows = int(np.ceil(num_plots / num_cols))
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	455
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	456 plots_data = create_plot_data(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	457 args.frac,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	458 args.it,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	459 args.num_bins,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	460 args.window_width,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	461 samples,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	462 num_samples,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	463 num_plots,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	464 num_cols,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	465 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	466
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	467 count_max = np.max([x.get("max_counts", 0) for x in plots_data])
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	468 log_fold_change_max = np.max([x.get("max_log_fold_change", 0) for x in plots_data])
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	469
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	470 ylim_hist = count_max * args.y_scale_factor
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	471 ylim_ma = log_fold_change_max * args.y_scale_factor
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	472
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	473 if args.interactive:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	474 fig = ma_plots_plotly(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	475 num_rows,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	476 num_cols,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	477 num_plots,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	478 plots_data,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	479 sample_names,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	480 args.size,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	481 ylim_hist,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	482 ylim_ma,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	483 features,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	484 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	485 fig.show()
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	486 if args.output_format == "html":
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	487 fig.write_html(f"{args.output_file}")
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	488 else:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	489 pio.write_image(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	490 fig,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	491 f"{args.output_file}",
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	492 format=args.output_format,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	493 width=args.size * num_cols,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	494 height=args.size * num_rows,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	495 scale=args.scale,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	496 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	497 else:
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	498 fig = ma_plots_matplotlib(
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	499 num_rows,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	500 num_cols,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	501 num_plots,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	502 plots_data,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	503 sample_names,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	504 args.size,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	505 ylim_hist,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	506 ylim_ma,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	507 args.window_width,
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	508 )
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	509 plt.show()
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	510 fig.savefig(f"{args.output_file}", format=args.output_format, dpi=300)
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	511 return 0
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	512
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	513
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	514 if __name__ == "__main__":
835867b8ebd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab iuc parents: diff changeset	515 main()

Mercurial > repos > iuc > maplot

annotate maplot.py @ 0:835867b8ebd9 draft default tip