VISET

Visual Itemized SET diagrams: area-proportional Venn/Euler and UpSet plots that print the member names inside each region, in Python.

Venn / Euler (three drugs)

Static (Matplotlib): proportional ellipses, every gene printed and auto-sized to fit its region.

import os
import matplotlib.pyplot as plt
from matplotlib import font_manager
from viset import load, eunoia_venn
fp = "Font" if os.path.isdir("Font") else "../Font"
for f in font_manager.findSystemFonts(fontpaths=[fp]):
    font_manager.fontManager.addfont(f)
db = "Drug target sample files/" if os.path.isdir("Drug target sample files") else "../Drug target sample files/"
def L(name, fname): return load(db + fname, "Gene names", name)
flx = L("Fluoxetine", "1. FLUOXETINE_sample.csv")
ibu = L("Ibuprofen", "2. IBUPROFEN_sample.csv")
ace = L("Acetaminophen", "3. ACETAMINOPHEN_sample.csv")
eunoia_venn([flx, ibu, ace], colors=["#3a7ca5", "#e08a3c", "#3c8c57"], style="round", title="", figsize=(8.5, 7.5), margin=0.06)

Interactive (Plotly): hover any region to read its members — the option to reach for when an intersection is too small for the static figure to fit its labels.

import os
import plotly.io as pio
pio.renderers.default = "notebook_connected"
from matplotlib import font_manager
from viset import load, eunoia_venn_interactive
fp = "Font" if os.path.isdir("Font") else "../Font"
for f in font_manager.findSystemFonts(fontpaths=[fp]):
    font_manager.fontManager.addfont(f)
db = "Drug target sample files/" if os.path.isdir("Drug target sample files") else "../Drug target sample files/"
def L(name, fname): return load(db + fname, "Gene names", name)
flx = L("Fluoxetine", "1. FLUOXETINE_sample.csv")
ibu = L("Ibuprofen", "2. IBUPROFEN_sample.csv")
ace = L("Acetaminophen", "3. ACETAMINOPHEN_sample.csv")
eunoia_venn_interactive([flx, ibu, ace], colors=["#3a7ca5", "#e08a3c", "#3c8c57"], width=760, height=680, title="")

UpSet (four drugs)

Static (Matplotlib): one bar per intersection with its members listed inside, so it keeps working past the three-set limit of a Venn.

import os
import matplotlib.pyplot as plt
from matplotlib import font_manager
from viset import load, upset
fp = "Font" if os.path.isdir("Font") else "../Font"
for f in font_manager.findSystemFonts(fontpaths=[fp]):
    font_manager.fontManager.addfont(f)
db = "Drug target sample files/" if os.path.isdir("Drug target sample files") else "../Drug target sample files/"
def L(name, fname): return load(db + fname, "Gene names", name)
ibu = L("Ibuprofen", "2. IBUPROFEN_sample.csv")
ace = L("Acetaminophen", "3. ACETAMINOPHEN_sample.csv")
dic = L("Diclofenac", "12. DICLOFENAC_sample.csv")
ind = L("Indomethacin", "13. INDOMETHACIN_sample.csv")
upset({"Ibuprofen": ibu, "Acetaminophen": ace, "Diclofenac": dic, "Indomethacin": ind},
      figsize=(13, 7), color_list="Set2", wspace=0.5)

Interactive (Plotly): hover any bar to read its members.

import os
import plotly.io as pio
pio.renderers.default = "notebook_connected"
from matplotlib import font_manager
from viset import load, upset_interactive
fp = "Font" if os.path.isdir("Font") else "../Font"
for f in font_manager.findSystemFonts(fontpaths=[fp]):
    font_manager.fontManager.addfont(f)
db = "Drug target sample files/" if os.path.isdir("Drug target sample files") else "../Drug target sample files/"
def L(name, fname): return load(db + fname, "Gene names", name)
ibu = L("Ibuprofen", "2. IBUPROFEN_sample.csv")
ace = L("Acetaminophen", "3. ACETAMINOPHEN_sample.csv")
dic = L("Diclofenac", "12. DICLOFENAC_sample.csv")
ind = L("Indomethacin", "13. INDOMETHACIN_sample.csv")
upset_interactive({"Ibuprofen": ibu, "Acetaminophen": ace, "Diclofenac": dic, "Indomethacin": ind}, wspace = 0.5, 
                  title="", color_list="Set2", figsize=(11, 6.5))

Want the reasoning behind all this? See State of current set diagrams for the existing tools and their gaps, and the Introduction to install VISET and run it on your own data. Full-page interactive versions: Venn and UpSet.