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worldmap_arabidopsis_admixed.py
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import altair as alt
from altair.expr import datum, substring
from vega_datasets import data
from sys import argv
import pandas as pd
df = pd.read_csv(argv[1])
df = df.dropna(subset=['longitude', 'latitude'])
countries = alt.topo_feature(data.world_110m.url, 'countries')
selection = alt.selection_multi(fields=['admixed group'])
color = alt.condition(selection,
alt.Color('admixed group:N', legend=None),
alt.value('#EEEEEE'))
brush = alt.selection_interval()
hover = alt.selection(type='single',
fields=["accession"])
chart = alt.Chart(countries).mark_geoshape(
fill='#CCCCCC',
stroke='white',
opacity=0.4
).properties(
width=850,
height=850
)
chart += alt.Chart(df).mark_circle(size=30, stroke="black", strokeWidth=0.3).encode(
longitude='longitude:Q',
latitude='latitude:Q',
color=color,
size=alt.condition(~hover, alt.value(30), alt.value(300)),
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by']
).project(type="orthographic").add_selection(hover).transform_filter(selection).transform_filter(brush)
text = alt.Chart(df).mark_text(align='right').encode(
alt.Text('name', type='nominal'),
longitude='longitude:Q',
latitude='latitude:Q',
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by'],
opacity=alt.condition(~hover, alt.value(0), alt.value(1))
).transform_filter(selection).transform_filter(brush).transform_filter(hover)
chart += text
chart_GTM = alt.Chart(df).mark_circle(size=30, strokeWidth=0.4).encode(
x=alt.X("GTM axis 1", axis=alt.Axis(
ticks=False, labels=False, grid=False)),
y=alt.Y("GTM axis 2", axis=alt.Axis(
ticks=False, labels=False, grid=False)),
color=color,
size=alt.condition(~hover, alt.value(30), alt.value(300)),
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by']
).properties(
width=250,
height=250,
).add_selection(brush).add_selection(hover)
text = alt.Chart(df).mark_text(align='right').encode(
alt.Text('name', type='nominal'),
x=alt.X("GTM axis 1"),
y=alt.Y("GTM axis 2"),
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by'],
opacity=alt.condition(~hover, alt.value(0), alt.value(1))
).transform_filter(selection).transform_filter(hover)
chart_GTM += text
chart_tSNE = alt.Chart(df).mark_circle(size=30, strokeWidth=0.4).encode(
x=alt.X("t-SNE axis 1", axis=alt.Axis(ticks=False, labels=False, grid=False)),
y=alt.Y("t-SNE axis 2", axis=alt.Axis(ticks=False, labels=False, grid=False)),
color=color,
size=alt.condition(~hover, alt.value(30), alt.value(300)),
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by']
).properties(
width=250,
height=250,
).add_selection(brush).add_selection(hover)
text = alt.Chart(df).mark_text(align='right').encode(
alt.Text('name', type='nominal'),
x=alt.X("t-SNE axis 1", axis=alt.Axis(ticks=False, labels=False, grid=False)),
y=alt.Y("t-SNE axis 2", axis=alt.Axis(ticks=False, labels=False, grid=False)),
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by'],
opacity=alt.condition(~hover, alt.value(0), alt.value(1))
).transform_filter(selection).transform_filter(hover)
chart_tSNE += text
chart_PCA = alt.Chart(df).mark_circle(size=30, strokeWidth=0.4).encode(
x=alt.X("Principal component 1", axis=alt.Axis(
ticks=False, labels=False, grid=False)),
y=alt.Y("Principal component 2", axis=alt.Axis(
ticks=False, labels=False, grid=False)),
color=color,
size=alt.condition(~hover, alt.value(30), alt.value(300)),
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by']
).properties(
width=250,
height=250,
).add_selection(brush).add_selection(hover)
text = alt.Chart(df).mark_text(align='right').encode(
alt.Text('name', type='nominal'),
x=alt.X("Principal component 1", axis=alt.Axis(
ticks=False, labels=False, grid=False)),
y=alt.Y("Principal component 2", axis=alt.Axis(
ticks=False, labels=False, grid=False)),
tooltip=['accession', 'name', 'country', 'admixed group',
'continent', 'country code', 'CS number',
'latitude', 'longitude',
'collector', 'site', 'seq by'],
opacity=alt.condition(~hover, alt.value(0), alt.value(1))
).transform_filter(selection).transform_filter(hover)
chart_PCA += text
legend = alt.Chart().mark_rect().encode(
y=alt.Y('admixed group:N', axis=alt.Axis(
orient='left', title="Admixed group")),
color=color
).add_selection(
selection
).transform_filter(brush)
hcharts = alt.hconcat(chart_GTM, chart_tSNE, chart_PCA, data=df)
chart = alt.hconcat(legend, chart, data=df)
vcharts = alt.vconcat(hcharts, chart, data=df
)
vcharts.save(argv[2]+'.html')