gistfile1.txt

from bokeh.plotting import figure, show
from pandas import read_csv
from bokeh.models.markers import marker_types
from bokeh.transform import factor_cmap, factor_mark

df = read_csv('samples/fishdata.csv')

all_markers = [mt for mt in marker_types]
SPECIES = list(set(df['species']))
MARKERS = all_markers[:len(SPECIES)]
feeds = list(set(df['feeds']))
p = figure(plot_height=600, plot_width=700,
        title = 
        'Metabolic variations based on 1H NMR profiling of fishes'
        )
p.xaxis.axis_label = 'Principal Component 1: 35.8%'
p.yaxis.axis_label = 'Principal Component 2: 15.1%'
p.scatter('PC1', 'PC2', source=df, size=12,
          fill_alpha=0.3, 
          marker=factor_mark('species', MARKERS, SPECIES),
          color=factor_cmap('feeds', 'Category10_3', feeds)
          )
output_notebook()
show(p)