Choropleth Africa map doesn’t show some countries and islands

I’m plotting an African continent map using choropleth. However, some regions are not appearing on the map, even the respective alpha codes being correct. For example, I have data from Seychelles (sov_a3="SYC"), Mauritius (sov_a3="MUS"), and the map is missing these regions or is not filled.

There is something I’m missing? I didn’t see a complete Africa map made with Plotly and I’m wondering if there is some issue with the parameter scope=“africa”

Follow below the code for the map and how it looks now.

fig_map = go.Figure(px.choropleth(df_map,
                            locations='sov_a3', color=map_count_column,
                            hover_name='country', animation_frame="date_2weeks",
                            color_continuous_scale="algae",
                            range_color=[0, max(df_map['cum_counts'])],
                            labels={'cum_counts': 'Number of genomes'}
                            ))
    fig_map.update_layout(geo_scope="africa")

Solution

it's all down to geometry / geojson. See documentation https://plotly.com/python/map-configuration/#physical-base-maps. Natural earth is used, which does not define these islands as part of Africa
have simulated a data frame for your code. To create MWE

import plotly.express as px
import plotly.graph_objects as go
import pandas as pd
import numpy as np

countries = 'TZA,ESH,COD,SOM,KEN,SDN,TCD,ZAF,LSO,ZWE,BWA,NAM,SEN,MLI,MRT,BEN,NER,NGA,CMR,TGO,GHA,CIV,GIN,GNB,LBR,SLE,BFA,CAF,COG,GAB,GNQ,ZMB,MWI,MOZ,SWZ,AGO,BDI,MDG,GMB,TUN,DZA,ERI,MAR,EGY,LBY,ETH,DJI,UGA,RWA,SSD'
names = "Tanzania,W. Sahara,Dem. Rep. Congo,Somalia,Kenya,Sudan,Chad,South Africa,Lesotho,Zimbabwe,Botswana,Namibia,Senegal,Mali,Mauritania,Benin,Niger,Nigeria,Cameroon,Togo,Ghana,Côte d'Ivoire,Guinea,Guinea-Bissau,Liberia,Sierra Leone,Burkina Faso,Central African Rep.,Congo,Gabon,Eq. Guinea,Zambia,Malawi,Mozambique,eSwatini,Angola,Burundi,Madagascar,Gambia,Tunisia,Algeria,Eritrea,Morocco,Egypt,Libya,Ethiopia,Djibouti,Uganda,Rwanda,S. Sudan"
# Seychelles (sov_a3="SYC"), Mauritius (sov_a3="MUS")
countries += ",SYC,MUS"
names += ",Seychelles,Mauritius"
map_count_column = "cum_counts"

# simulate implied dataframe in question
df_map = (
    pd.DataFrame({"sov_a3": countries.split(","),"country":names.split(",")})
    .merge(pd.DataFrame({"date_2weeks": list("ABC")}), how="cross")
    .assign(
        cum_counts=lambda d: np.random.randint(1, 5, len(d)),
    )
)

# go.Figure is spurious remove
fig_map = px.choropleth(
    df_map,
    locations="sov_a3",
    color=map_count_column,
    hover_name="country",
    animation_frame="date_2weeks",
    color_continuous_scale="algae",
    range_color=[0, max(df_map["cum_counts"])],
    labels={"cum_counts": "Number of genomes"},
)
fig_map.update_layout(geo_scope="africa")

now I use a different geojson where the islands are defined. However this is imperfect as I have not ensured names map correctly to geojson
this does show Mauritius

import requests
res = requests.get("https://raw.githubusercontent.com/codeforgermany/click_that_hood/main/public/data/africa.geojson")

# use out own geometry
fig_map = px.choropleth(
    df_map,
    geojson=res.json(),
    locations="country",
    featureidkey="properties.name",
    color=map_count_column,
    hover_name="country",
    animation_frame="date_2weeks",
    color_continuous_scale="algae",
    range_color=[0, max(df_map["cum_counts"])],
    labels={"cum_counts": "Number of genomes"},
)

fig_map.update_geos(fitbounds="locations")