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# Firstly, we need to import all the required packages: | |
import streamlit as st | |
import csv | |
import numpy as np | |
import pandas as pd | |
import matplotlib.pyplot as plt | |
import seaborn as sns | |
import gseapy as gp | |
import plotly.express as px | |
from scipy.stats import pearsonr | |
from sklearn import linear_model, metrics | |
from sklearn.datasets import * | |
from scipy import stats | |
import plotly.graph_objects as go | |
import plotly.figure_factory as ff | |
import re | |
from scipy.spatial.distance import pdist, squareform | |
from dash import dcc | |
import dash_bio as dashbio | |
# You may use the following code to make the layout wider. It should be the first code you use. | |
st.set_page_config(layout="wide") | |
# Next, we type in the codes needed to read your selected dataset. Prepare a .csv file beforehand with the specific timepoint that you are interested in. We will use Pandas to read and load that .csv file into Streamlit. You can also include a title for easier visualisation. | |
st.title("Analysis using the adenovirus seronegative dataset for 1d vs 0") | |
Ad5_seroneg = pd.read_csv('/Users/gabri/Desktop/vaccine/dashboarding/Ad5_Zak_1dvs0.csv', index_col=0) | |
Ad5_seroneg | |
# The first part of our analysis will be to find the upregulated and downregulated DEGs | |
st.subheader("Upregulated and Downregulated DEGs") | |
Ad5_seroneg['pval_1dvs0'] = pd.to_numeric(Ad5_seroneg['pval_1dvs0'], errors = 'coerce') | |
Ad5_seroneg['qval_1dvs0'] = pd.to_numeric(Ad5_seroneg['qval_1dvs0'], errors = 'coerce') | |
# We use the following command to filter the DEGs based on adjusted p-value < 0.05 and your chosen fold change value. | |
Ad5_seroneg_DEGs_up_FC_1pt3_FDRpval_pt05 = Ad5_seroneg[(Ad5_seroneg["fc_1dvs0"] > 1.3) & (Ad5_seroneg["qval_1dvs0"] < 0.05)] | |
Ad5_seroneg_DEGs_up_FC_1pt3_FDRpval_pt05_counts = Ad5_seroneg_DEGs_up_FC_1pt3_FDRpval_pt05.index | |
Ad5_seroneg_DEGs_down_FC_1pt3_FDRpval_pt05 = Ad5_seroneg[(Ad5_seroneg["fc_1dvs0"] < -1.3) & (Ad5_seroneg["qval_1dvs0"] < 0.05)] | |
Ad5_seroneg_DEGs_down_FC_1pt3_FDRpval_pt05_counts = Ad5_seroneg_DEGs_down_FC_1pt3_FDRpval_pt05.index |
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