| import dash | |
| import dash_core_components as dcc | |
| import dash_html_components as html | |
| import dash_bio | |
| import pandas as pd | |
| import kegg2cyjs | |
| import plotly.graph_objs as go | |
| # df = pd.read_csv("./ecoliLeucineRMA.csv") |
| import pandas as pd | |
| df = pd.read_csv("./eLeuRMA.txt", sep='\t') | |
| gene_df = df[df['Unnamed: 0'].str.contains(pat='b[0-9]{4}')] | |
| foo = gene_df['Unnamed: 0'].str.extract(r'(b[0-9]{4})') | |
| foo = foo[0].str.replace("b", "eco:b") | |
| gene_df.update(foo.rename('Unnamed: 0')) | |
| gene_df.columns = gene_df.columns.str.replace("/home/laurent/Affymetrix_data/ecoli_sample//", "") | |
| gene_df.columns = gene_df.columns.str.replace("Unnamed: 0", "keggids") | |
| gene_df.to_csv('ecoliLeucineRMA.csv', index=False) |
| library(ecoliLeucine) | |
| data("ecoliLeucine") | |
| library(affy) | |
| eset <- rma(ecoliLeucine) | |
| write.exprs(eset, "eLeuRMA.txt") |
| [ { | |
| "format_version" : "1.0", | |
| "generated_by" : "cytoscape-3.7.1", | |
| "target_cytoscapejs_version" : "~2.1", | |
| "title" : "KEGG style", | |
| "style" : [ { | |
| "selector" : "node", | |
| "css" : { | |
| "font-family" : "Dialog.plain", | |
| "font-weight" : "normal", |
| package: | |
| name: ecell | |
| version: "4.1.4" | |
| build: | |
| number: 0 | |
| skip: True # [win32] | |
| skip: True # [win64 and py<35] | |
| skip: True # [osx and py34] | |
| skip: True # [py26] | |
| skip: True # [py33] |
Here are two extremely simple examples, See http://ecell4.readthedocs.org for more details on running E-Cell4.
Python 2.7.6 (default, Mar 22 2014, 22:59:56)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from ecell4.core import *
| kgml = requests.get('http://rest.kegg.jp/get/mmu04150/kgml').content | |
| soup = BeautifulSoup(kgml, "xml") | |
| entries = soup.find_all('entry') | |
| len(entries) | |
| d = {} | |
| elements = {} | |
| nodes = [] | |
| edges = [] |
Content entered directly below the header but before the first section heading is called the preamble.
| # | |
| # This is a Shiny web application. You can run the application by clicking | |
| # the 'Run App' button above. | |
| # | |
| # Find out more about building applications with Shiny here: | |
| # | |
| # http://shiny.rstudio.com/ | |
| # | |
| library(shiny) |