Change errorbar thickness in Altair - python

How can I change the thickness of my errorbars in Altair?
When I tried to change the color to black, it turns out than it should be.
Why is that?
My expected output is
But the actual output is
Here is my code
import altair as alt
alt.Chart(df2).mark_errorbar(color='black').encode(
alt.X(
"quantile95",
axis=alt.Axis(title="lower",tickMinStep=5),
scale=alt.Scale(domain=[0, 55])
)
).properties(width=450, height=20)

Since no data was provided, I used the data from the official reference to create the expected output.
One is a box plot and the other is an overlaid strip plot.
import altair as alt
from vega_datasets import data
source = data.barley()
error_bar_s = alt.Chart(source).mark_boxplot(color='black').encode(
x=alt.X("yield:Q", axis=alt.Axis(title="lower", tickMinStep=5), scale=alt.Scale(domain=[0, source['yield'].max()+10])),
y=alt.Y('variety:N')
).properties(width=450, height=450)
strip = alt.Chart(source).mark_tick(color='red').encode(
x='yield:Q',
y='variety:N'
)
error_bar_s + strip

Using Iris dataset as example this will be the necessary code
from vega_datasets import data # pip install vega_datasets
import altair as alt
dataset = data.iris()
ticks = alt.Chart(dataset).mark_tick().encode(
alt.X('sepalWidth', scale=alt.Scale(zero=False)),
)
mean_point = alt.Chart(dataset).mark_circle().encode(
x=alt.X('mean(sepalWidth)'),
color=alt.value("black"),
size=alt.value(50)
)
errorbar = alt.Chart(dataset).mark_errorbar(extent='stdev', ticks=True).encode(
x=alt.X('sepalWidth'),
color=alt.value("black"),
strokeWidth=alt.value(5)
)
errorbar + mean_point + ticks
Output:
Some key remarks:
If ticks are not needed, remove the ticks parameter in the mark_errobar
The "thickness" of the CI is the strokeWidth parameter in the encode of the mark_errorbar
The extend parameter could be "ci", "stdev", "stderr", "iqr". See docs

Related

Parallel coordinates in Altair

I want to do a parallel coordinates plot with multiple y axis. I've found how to do it in Vega-Lite here but I haven't found the way to do it with Altair, there's only a very simple example where all the y axis are the same.
Is there any way to do this plot in altair?
Note that this kind of chart is not "built-in" to Altair or Vega-Lite, so the only way to create it is with a manual sequence of transforms, and manually constructing your axes from tick and text marks.
Here is an Altair version of the chart in the answer you linked to:
import altair as alt
from vega_datasets import data
base = alt.Chart(
data.iris.url
).transform_window(
index="count()"
).transform_fold(
["petalLength", "petalWidth", "sepalLength", "sepalWidth"]
).transform_joinaggregate(
min="min(value)",
max="max(value)",
groupby=["key"]
).transform_calculate(
norm_val="(datum.value - datum.min) / (datum.max - datum.min)",
mid="(datum.min + datum.max) / 2"
).properties(width=600, height=300)
lines = base.mark_line(opacity=0.3).encode(
x='key:N',
y=alt.Y('norm_val:Q', axis=None),
color="species:N",
detail="index:N",
tooltip=["petalLength:N", "petalWidth:N", "sepalLength:N", "sepalWidth:N"]
)
rules = base.mark_rule(
color="#ccc", tooltip=None
).encode(
x="key:N",
detail="count():Q",
)
def ytick(yvalue, field):
scale = base.encode(x='key:N', y=alt.value(yvalue), text=f"min({field}):Q")
return alt.layer(
scale.mark_text(baseline="middle", align="right", dx=-5, tooltip=None),
scale.mark_tick(size=8, color="#ccc", orient="horizontal", tooltip=None)
)
alt.layer(
lines, rules, ytick(0, "max"), ytick(150, "mid"), ytick(300, "min")
).configure_axisX(
domain=False, labelAngle=0, tickColor="#ccc", title=None
).configure_view(
stroke=None
)

How to color lines on mouseover in a bump chart using Altair Viz?

The goal is to highlight the entire line when hovering anywhere (not just at the data points) on the line.
Imports:
from IPython.display import display
import pandas as pd
import altair as alt
Data:
data = '{"Date":{"5":1560643200000,"18":1560643200000,"22":1560643200000,"24":1560643200000,"59":1560643200000,"65":1561248000000,"78":1561248000000,"82":1561248000000,"84":1561248000000,"119":1561248000000,"125":1561852800000,"138":1561852800000,"142":1561852800000,"144":1561852800000,"179":1561852800000,"185":1562457600000,"198":1562457600000,"202":1562457600000,"204":1562457600000,"239":1562457600000,"245":1563062400000,"258":1563062400000,"262":1563062400000,"264":1563062400000,"299":1563062400000,"305":1563667200000,"318":1563667200000,"322":1563667200000,"324":1563667200000,"359":1563667200000,"365":1564272000000,"378":1564272000000,"382":1564272000000,"384":1564272000000,"419":1564272000000,"425":1564876800000,"438":1564876800000,"442":1564876800000,"444":1564876800000,"479":1564876800000,"485":1565481600000,"498":1565481600000,"502":1565481600000,"504":1565481600000,"539":1565481600000,"545":1566086400000,"558":1566086400000,"562":1566086400000,"564":1566086400000,"599":1566086400000,"605":1566691200000,"618":1566691200000,"622":1566691200000,"624":1566691200000,"659":1566691200000,"665":1567296000000,"678":1567296000000,"682":1567296000000,"684":1567296000000,"719":1567296000000,"725":1567900800000,"738":1567900800000,"742":1567900800000,"744":1567900800000,"779":1567900800000,"785":1568505600000,"798":1568505600000,"802":1568505600000,"804":1568505600000,"839":1568505600000,"845":1569110400000,"858":1569110400000,"862":1569110400000,"864":1569110400000,"899":1569110400000,"905":1569715200000,"918":1569715200000,"922":1569715200000,"924":1569715200000,"959":1569715200000,"965":1570320000000,"978":1570320000000,"982":1570320000000,"984":1570320000000,"1019":1570320000000,"1025":1570924800000,"1038":1570924800000,"1042":1570924800000,"1044":1570924800000,"1079":1570924800000,"1085":1571529600000,"1098":1571529600000,"1102":1571529600000,"1104":1571529600000,"1139":1571529600000,"1145":1572134400000,"1158":1572134400000,"1162":1572134400000,"1164":1572134400000,"1199":1572134400000,"1205":1572739200000,"1218":1572739200000,"1222":1572739200000,"1224":1572739200000,"1259":1572739200000,"1265":1573344000000,"1278":1573344000000,"1282":1573344000000,"1284":1573344000000,"1319":1573344000000,"1325":1573948800000,"1338":1573948800000,"1342":1573948800000,"1344":1573948800000,"1379":1573948800000,"1385":1574553600000,"1398":1574553600000,"1402":1574553600000,"1404":1574553600000,"1439":1574553600000,"1445":1575158400000,"1458":1575158400000,"1462":1575158400000,"1464":1575158400000,"1499":1575158400000,"1505":1575763200000,"1518":1575763200000,"1522":1575763200000,"1524":1575763200000,"1559":1575763200000,"1565":1576368000000,"1578":1576368000000,"1582":1576368000000,"1584":1576368000000,"1619":1576368000000},"Store":{"5":"store1","18":"store2","22":"store3","24":"store4","59":"store5","65":"store1","78":"store2","82":"store3","84":"store4","119":"store5","125":"store1","138":"store2","142":"store3","144":"store4","179":"store5","185":"store1","198":"store2","202":"store3","204":"store4","239":"store5","245":"store1","258":"store2","262":"store3","264":"store4","299":"store5","305":"store1","318":"store2","322":"store3","324":"store4","359":"store5","365":"store1","378":"store2","382":"store3","384":"store4","419":"store5","425":"store1","438":"store2","442":"store3","444":"store4","479":"store5","485":"store1","498":"store2","502":"store3","504":"store4","539":"store5","545":"store1","558":"store2","562":"store3","564":"store4","599":"store5","605":"store1","618":"store2","622":"store3","624":"store4","659":"store5","665":"store1","678":"store2","682":"store3","684":"store4","719":"store5","725":"store1","738":"store2","742":"store3","744":"store4","779":"store5","785":"store1","798":"store2","802":"store3","804":"store4","839":"store5","845":"store1","858":"store2","862":"store3","864":"store4","899":"store5","905":"store1","918":"store2","922":"store3","924":"store4","959":"store5","965":"store1","978":"store2","982":"store3","984":"store4","1019":"store5","1025":"store1","1038":"store2","1042":"store3","1044":"store4","1079":"store5","1085":"store1","1098":"store2","1102":"store3","1104":"store4","1139":"store5","1145":"store1","1158":"store2","1162":"store3","1164":"store4","1199":"store5","1205":"store1","1218":"store2","1222":"store3","1224":"store4","1259":"store5","1265":"store1","1278":"store2","1282":"store3","1284":"store4","1319":"store5","1325":"store1","1338":"store2","1342":"store3","1344":"store4","1379":"store5","1385":"store1","1398":"store2","1402":"store3","1404":"store4","1439":"store5","1445":"store1","1458":"store2","1462":"store3","1464":"store4","1499":"store5","1505":"store1","1518":"store2","1522":"store3","1524":"store4","1559":"store5","1565":"store1","1578":"store2","1582":"store3","1584":"store4","1619":"store5"},"Rank":{"5":1.0,"18":1.0,"22":1.0,"24":1.0,"59":1.0,"65":2.0,"78":2.0,"82":2.0,"84":2.0,"119":2.0,"125":2.0,"138":2.0,"142":2.0,"144":2.0,"179":2.0,"185":2.0,"198":2.0,"202":2.0,"204":2.0,"239":2.0,"245":2.0,"258":2.0,"262":2.0,"264":2.0,"299":2.0,"305":2.0,"318":2.0,"322":2.0,"324":2.0,"359":2.0,"365":2.0,"378":2.0,"382":2.0,"384":1.0,"419":2.0,"425":3.0,"438":1.0,"442":3.0,"444":2.0,"479":3.0,"485":4.0,"498":1.0,"502":4.0,"504":3.0,"539":4.0,"545":4.0,"558":1.0,"562":3.0,"564":3.0,"599":4.0,"605":5.0,"618":1.0,"622":2.0,"624":4.0,"659":5.0,"665":6.0,"678":1.0,"682":2.0,"684":5.0,"719":6.0,"725":7.0,"738":1.0,"742":2.0,"744":5.0,"779":7.0,"785":8.0,"798":1.0,"802":2.0,"804":6.0,"839":8.0,"845":8.0,"858":1.0,"862":2.0,"864":5.0,"899":8.0,"905":8.0,"918":1.0,"922":2.0,"924":4.0,"959":8.0,"965":8.0,"978":1.0,"982":2.0,"984":4.0,"1019":8.0,"1025":10.0,"1038":1.0,"1042":2.0,"1044":5.0,"1079":10.0,"1085":10.0,"1098":1.0,"1102":2.0,"1104":5.0,"1139":10.0,"1145":11.0,"1158":1.0,"1162":2.0,"1164":5.0,"1199":11.0,"1205":12.0,"1218":1.0,"1222":2.0,"1224":6.0,"1259":12.0,"1265":13.0,"1278":2.0,"1282":1.0,"1284":7.0,"1319":13.0,"1325":13.0,"1338":2.0,"1342":1.0,"1344":6.0,"1379":13.0,"1385":14.0,"1398":2.0,"1402":1.0,"1404":6.0,"1439":14.0,"1445":3.0,"1458":2.0,"1462":1.0,"1464":6.0,"1499":8.0,"1505":3.0,"1518":2.0,"1522":1.0,"1524":6.0,"1559":4.0,"1565":3.0,"1578":2.0,"1582":1.0,"1584":8.0,"1619":5.0}}'
Dataframe:
df_slim = pd.read_json(data)
Chart:
highlight = alt.selection(type='single', on='mouseover',
fields=['Store'], nearest=True, empty="none")
chart = alt.Chart(df_slim).mark_line().encode(
x='Date',
y='Rank',
#color='Store',
strokeDash='Store',
color=alt.condition(highlight, 'Store', alt.value("lightgray")),
tooltip=['Rank','Store']
).properties(
width=800,
height=600,
title='Bump Chart: Store Ranking'
).configure_title(
fontSize=30,
font='Courier',
anchor='start',
color='gray'
).add_selection(
highlight
)
display(chart)
Output:
Any help? Not sure what went wrong here.
Good question! It turns out this is one of the current limitations of Vega-Lite. I found this note in the VL docs on Nearest Value
The nearest transform is not supported for continuous mark types (i.e., line and area). For these mark types, consider layering a discrete mark type (e.g., point) with a 0-value opacity
So for your example I would do something like this
highlight = alt.selection(type='single', on='mouseover',
fields=['Store'], nearest=True, empty="none")
chart = alt.Chart(df_slim).mark_line().encode(
x='Date',
y='Rank',
#color='Store',
strokeDash='Store',
color=alt.condition(highlight, 'Store', alt.value("lightgray")),
tooltip=['Rank','Store']
)
points = alt.Chart(df_slim).mark_point(opacity=0).encode(
x='Date',
y='Rank',).add_selection(
highlight
)
chart + points

Adding legend to layerd chart in altair

Consider the following example:
import altair as alt
from vega_datasets import data
df = data.seattle_weather()
temp_max = alt.Chart(df).mark_line(color='blue').encode(
x='yearmonth(date):T',
y='max(temp_max)',
)
temp_min = alt.Chart(df).mark_line(color='red').encode(
x='yearmonth(date):T',
y='max(temp_min)',
)
temp_max + temp_min
In the resulting chart, I would like to add a legend that shows, that the blue line shows the maximum temperature and the red line the minimum temperature. What would be the easiest way to achieve this?
I saw (e.g. in the solution to this question: Labelling Layered Charts in Altair (Python)) that altair only adds a legend if in the encoding, you set the color or size or so, usually with a categorical column, but that is not possible here because I'm plotting the whole column and the label should be the column name (which is now shown in the y-axis label).
I would do a fold transform such that the variables could be encoded correctly.
import altair as alt
from vega_datasets import data
df = data.seattle_weather()
alt.Chart(df).mark_line().transform_fold(
fold=['temp_max', 'temp_min'],
as_=['variable', 'value']
).encode(
x='yearmonth(date):T',
y='max(value):Q',
color='variable:N'
)
If you layer two charts with the same columns and tell them to color by the same one, the legend will appear. Don't know is this helps but..
For example, i had:
Range, Amount, Type
0_5, 3, 'Private'
5_10, 5, 'Private'
Range, Amount, Type
0_5, 3, 'Public'
5_10, 5, 'Public'
and I charted both with 'color = 'Type'' and said alt.layer(chart1, chart2) and it showed me a proper legend

Format Altair choropleth map color scale

I am trying to encode percentage with a color scale on a choropleth map. How can I format the scale to show percent values (ex. 10%) rather than fraction values (ex. 0.1)? I know for a regular X or Y axis you could do axis=alt.Axis(format='.0%'), but I can't see how to use formatting for this color scale.
import altair as alt
import pandas as pd
from vega_datasets import data
alt.renderers.enable('notebook')
airports = pd.read_csv(data.airports.url)
airports = airports.groupby('state').agg({'iata': 'count'})
airports['id'] = range(1, len(airports) + 1)
airports['pct'] = airports['iata'] / airports['iata'].sum()
states = alt.topo_feature(data.us_10m.url, feature='states')
alt.Chart(states).mark_geoshape().encode(
color='pct:Q'
).transform_lookup(
lookup='id',
from_=alt.LookupData(airports, 'id', ['pct'])
).project('albersUsa')
The legend attribute of the color encoding accepts a format argument that controls the format of the legend's scale:
alt.Chart(states).mark_geoshape().encode(
color=alt.Color('pct:Q', legend=alt.Legend(format=".0%"))
).transform_lookup(
lookup='id',
from_=alt.LookupData(airports, 'id', ['pct'])
).project('albersUsa')
More info in the alt.Legend documentation.

Invert axis direction Altair

For some reason, the Y-axis while plotting with altair seems to be inverted (would expect values to go from lower (bottom) to higher (top) of the plot). Also, I would like to be able to change the ticks frequency. With older versions I could use ticks=n_ticks but it seems now this argument can take only boolean.
import altair as alt
alt.renderers.enable('notebook')
eff_metals = pd.read_excel(filename, sheet_name='summary_eff_metals')
points = alt.Chart(eff_metals, height=250, width=400).mark_circle().encode(
x=alt.X('Temperature:Q',axis=alt.Axis(title='Temperature (°C)'),
scale=alt.Scale(zero=False, padding=50)),
y=alt.Y('Efficiency:N',axis=alt.Axis(title='Efficiency (%)'),
scale=alt.Scale(zero=False, padding=1)),
color=alt.Color('Element:N'),
)
text = points.mark_text(align='right', dx=0, dy=-5).encode(
text='Element:N'
)
chart = alt.layer(points, text, data=eff_metals,
width=600, height=300)
chart
And the figure:
I don't have your data, so difficult to write working code.
But here's an example of an inverted scale with additional ticks that is similar to the example scatter with tooltips example. See here for it in the vega editor.
import altair as alt
from vega_datasets import data
iris = data.iris()
alt.Chart(iris).mark_point().encode(
x='petalWidth',
y=alt.Y('petalLength', scale=alt.Scale(domain=[7,0]), axis=alt.Axis(tickCount=100)),
color='species'
).interactive()
This might work with your data:
eff_metals = pd.read_excel(filename, sheet_name='summary_eff_metals')
points = alt.Chart(eff_metals, height=250, width=400).mark_circle().encode(
x=alt.X('Temperature:Q',axis=alt.Axis(title='Temperature (°C)'),
scale=alt.Scale(zero=False, padding=50)),
y=alt.Y('Efficiency:N',axis=alt.Axis(title='Efficiency (%)'),
scale=alt.Scale(zero=False, padding=1, domain=[17,1])),
color=alt.Color('Element:N'),
)
text = points.mark_text(align='right', dx=0, dy=-5).encode(
text='Element:N'
)
chart = alt.layer(points, text, data=eff_metals,
width=600, height=300)
chart
However, I think it's possible that you've might just have the wrong type on your efficiency variable. You could try and replace 'Efficiency:N' with `'Efficiency:Q' and that might do it?
While it's possible to reverse the domain manually, that requires hardcoding the bounds.
Instead we can just pass Scale(reverse=True) to the axis encoding, e.g.:
from vega_datasets import data
alt.Chart(data.wheat().head()).mark_bar().encode(
x='wheat:Q',
y=alt.Y('year:O', scale=alt.Scale(reverse=True)),
)
Here it's been passed to alt.Y, so the years are inverted (left) vs the default y='year:O' (right):

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