Refactoring of the repo

ClinMicro/README.md

@@ -1,11 +1,11 @@
+> **Status:** Manually run whenever there is new data.
+
 ## Scripts related to clinical microbiology
 
-This folder contains all the initial files required to produce the visualisations shown on the page for the clinical microbiology dashboard on the portal.
+This folder contains all of the scripts required to produce the visualisations shown on the [SARS-CoV-2 variants for Uppsala](https://www.pathogens.se/dashboards/variants_region_uppsala/) dashboard on the portal. The data are held offline. All of the scripts use the global requirements file for the visualisations repository that contains this subfolder.
 
 **lineage_five_recent.py** - script to prepare the data and produce the graph for lineages classified according to their Pango lineage more granularly than in the 'four' lineage plot. Data are limited to the period since October 2023.
 
 **lineage_four_recent.py** - script to prepare the data and produce the graph for lineages classified according to their Pango lineage. Data are limited to the period since the start of 2023.
 
 **lineage_one_wholetime.py** - script to prepare the data and produce the graph for lineages classified according to their WHO classification and/or Pango lineage. Shows data from the full timeline.
-
-**requirements.txt** - requirements file showing packages used.

Count_publications/README.md

@@ -1,9 +1,7 @@
-## Count_publications
+>**Status:** Active, automatically run in `dc-dynamic`'s [runner_weekly.sh](https://github.com/ScilifelabDataCentre/dc-dynamic/blob/master/runner_weekly.sh)
 
-This folder contains the information required to create the plot related to counts of publications in the COVID-19 publication database. It comprises of a combined line and bar plot. Note that this plot is set up in the dynamic repository to automatically update.
+## Count_publications
 
-**gitignore** - a gitignore file for this part of the reporsitory.
+This folder contains the information required to create the plot related to counts of publications in the COVID-19 publication database and showed in [COVID-19 publication overview](https://www.pathogens.se/dashboards/covid_publications/) dashboard. It comprises of a combined line and bar plot. Note that this plot is set up in the dynamic repository to automatically update.
 
 **count_publications.py** - the script used to produce the plot.
-
-**requirements.txt** - the requirements file used to recreate the environment needed to run the python script.

Count_publications/count_publications.py

@@ -21,7 +21,7 @@
 df = df[df["published"] < currdate]
 df.sort_values(by="published", inplace=True)
 df1 = df["published"].value_counts().sort_index().reset_index()
-df1["cumulativecount"] = df1["published"].cumsum()
+df1["cumulativecount"] = df1["count"].cumsum()
 
 # find number of papers published in each month
 df["year"] = pd.DatetimeIndex(df["published"]).year
@@ -42,7 +42,7 @@
 # line graph
 trace1 = go.Scatter(
     mode="lines",
-    x=df1["index"],
+    x=df1["published"],
     y=df1["cumulativecount"],
     name="Cumulative Total",
     marker_color="rgb(46,104,165)",