This repository holds the inital visualisation scripts produced for the Swedish Pathogens Portal, and some other scripts for plots under development. Some of the scripts here are also used in the dynamic repository, where they are used in cron jobs so that the plots update automatically.
This folder contains old code that are not used anymore, but kept for reference if needed.
This folder contains all of the scripts and associated files required to produce the visualisations displayed on the SARS-CoV-2 variants dashboard, that were produced in plotly using python.
Status: Active, manually run whenever there is new data.
This folder contains the code used to produce 'live' counts of the monthly cumulative number of publications in the COVID-19 publication overview dashboard. These are included as a line and bar plot on the same graph, respectively.
Status: Active, automatically run in dc-dynamic's runner_weekly.sh
This folder contains the scripts and associated files required to produce the choropleth maps used to display the data from the symptoms app on the Symptoms study dashboard.
Status: Historic, data not updated anymore
This folder contains all of the scripts and associated files required to produce the visualisations displayed on the NPC test statistics dashboard, that were produced in plotly using python.
Status: Historic, data not updated anymore
This repository contains the script that can be used to generate a summary of the Swedish population from publicly available data from https://www.scb.se/. The data is updated each quarter, but not on a consistent date. The script generates a summary excel file should be updated in blobserver here for use in calculations related to the vaccinations and postcovid pages of the portal.
Status: Still relavant as RECOVAC dashboard might be updated
This folder contains all of the scripts and associated files required to produce the visualisations displayed on the postcovid dashboard of the portal. The folder contains scripts to complete data manipulations and produce choropleth maps.
Status: Historic, data not updated anymore
This folder contains all of the scripts and associated data required to produce the visualisations on the RECOVAC dashboard of the portal. It includes bar charts and area under the curve plots. The data are provided by the RECOVAC project.
Status: Active, manually run whenever there is new data.
This folder contains all of the scripts and associated data required to produce the visualisations on the serology tests dashboard of the portal. It includes bar charts and area under the curve plots. The data are provided by the SciLifeLab Autoimmunity and Serology Profiling unit.
Status: Active, automatically run in dc-dynamic's runner_every10mins.sh
This folder contains all of the scripts and associated data required to produce the visualisations on the vaccine administration dashboard of the portal. It includes bar charts, heatmaps and choropleth maps.
Status: Historic, data not updated anymore
This folder contains all of the plots on the wastewater page that were created using plotly in python. This includes the 'combined' graphs, showing data from multiple areas displayed on both a linear and log scale.
Status: Active, automatically run in dc-dynamic's runner_every10mins.sh
The wordcloud folder contains python script that can be used to generate a 'live' word cloud from the Covid-19 publications data, which is used in COVID-19 publication overview dashboard. It also includes the font to be used as standard for the portal, a square shape that can be used as the 'mask' for the wordcloud (mask defines the shape) and a folder of example wordclouds.
Status: Active, automatically run in dc-dynamic's runner_weekly.sh