Modified legend key and created dictionary for codelist

Author: viv3ckj

analysis/report_measures.py

@@ -15,34 +15,28 @@
     # Pharmacy First service (qualifier value)
     "pharmacy_first_service": ["983341000000102"],
 }
-# The following codes come from codelists/user-chriswood-pharmacy-first-clinical-pathway-conditions.csv file.
-# Currently written as a hardcoded dictionary to allow for easy for looping (ln66-83), but will be imported from codelist csv in future commits.
-# Pharmacy First seven clinical conditions codelist
-pharmacy_first_conditions_codes = {
-    # Community Pharmacy (CP) Blood Pressure (BP) Check Service (procedure)
-    "acute_otitis_media": ["3110003"],
-    # Community Pharmacy (CP) Contraception Service (procedure)
-    "herpes_zoster": ["4740000"],
-    # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
-    "acute_sinusitis": ["15805002"],
-    # Pharmacy First service (qualifier value)
-    "impetigo": ["48277006"],
-    # Community Pharmacy (CP) Contraception Service (procedure)
-    "infected_insect_bite": ["262550002"],
-    # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
-    "acute_pharyngitis": ["363746003"],
-    # Pharmacy First service (qualifier value)
-    "uncomplicated_urinary_tract_infection": ["1090711000000102"],
-}
 
+# Import the codelist from CSV
+pharmacy_first_codelist = codelist_from_csv(
+    "codelists/user-chriswood-pharmacy-first-clinical-pathway-conditions.csv",
+    column="code", category_column = "term"
+)
+
+pharmacy_first_conditions_codes = {}
+# Iterate through codelist, forming a dictionary 
+for codes, term in pharmacy_first_codelist.items():
+    normalised_term = term.lower().replace(" ", "_")
+    codes = [codes]
+    pharmacy_first_conditions_codes[normalised_term] = codes
+    
 registration = practice_registrations.for_patient_on(INTERVAL.end_date)
 
 # Select clinical events in interval date range
 selected_events = clinical_events.where(
     clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
 )
 
-# Loop through each condition to create a measure
+# Loop through each CLINICAL SERVICE to create a measure
 for pharmacy_first_event, codelist in pharmacy_first_event_codes.items():
     condition_events = selected_events.where(
         clinical_events.snomedct_code.is_in(codelist)
@@ -51,7 +45,6 @@
     # Define the numerator as the count of events for the condition
     numerator = condition_events.count_for_patient()
 
-
     # Define the denominator as the number of patients registered
     denominator = registration.exists_for_patient()
 
@@ -62,7 +55,7 @@
         intervals=months(8).starting_on("2023-11-01")
     )
 
-# Loop through each CLINICAL condition to create a measure
+# Loop through each CLINICAL CONDITION to create a measure
 for condition_name, condition_code in pharmacy_first_conditions_codes.items():
     condition_events = selected_events.where(
         clinical_events.snomedct_code.is_in(condition_code)
@@ -71,7 +64,6 @@
     # Define the numerator as the count of events for the condition
     numerator = condition_events.count_for_patient()
 
-
     # Define the denominator as the number of patients registered
     denominator = registration.exists_for_patient()
 

analysis/reports/pf_report.Rmd

@@ -94,12 +94,32 @@ df_measures <- readr::read_csv(
   here::here("output", "report", "conditions_measures.csv")
 )
 
+# Define the custom labels for clinical conditions
+clinical_measure_labels <- c(
+  "count_acute_otitis_media" = "Acute Otitis Media",
+  "count_herpes_zoster" = "Herpes Zoster",
+  "count_acute_sinusitis" = "Acute Sinusitis", 
+  "count_impetigo" = "Impetigo",
+  "count_infected_insect_bite" = "Infected Insect Bite",
+  "count_acute_pharyngitis" = "Acute Pharyngitis",
+  "count_uncomplicated_urinary_tract_infection" = "UTI"
+)
+
+# Define the custom labels for clinical services
+clinical_service_labels <- c(
+  "count_blood_pressure_service" = "Blood Pressure Service", 
+  "count_contraception_service" = "Contraception Service", 
+  "count_consultation_service" = "Consultation Service", 
+  "count_pharmacy_first_service" = "Pharmacy First Service"
+)
+
+```
+
+```{r, message=FALSE, warning=FALSE}
 plot_services <- plot_measures(df_measures,
 title = "Number of consultations for each clinical service per month",
-measure_names = c("count_blood_pressure_service", 
-                "count_contraception_service", 
-                "count_consultation_service", 
-                "count_pharmacy_first_service"),
+measure_names = names(clinical_service_labels),
+custom_labels = clinical_service_labels,
 y_label = "Number of codes for consultations",
 )
 print(plot_services)
@@ -123,13 +143,8 @@ Here we show the number of consultations for each of the Pharmacy First Clinical
 
 plot_conditions <- plot_measures(df_measures,
 title = "Number of consultations for each clinical condition per month",
-measure_names = c("count_acute_otitis_media", 
-                  "count_herpes_zoster", 
-                  "count_acute_sinusitis", 
-                  "count_impetigo",
-                  "count_infected_insect_bite",
-                  "count_acute_pharyngitis",
-                  "count_uncomplicated_urinary_tract_infection"),
+measure_names = names(clinical_measure_labels),
+custom_labels = clinical_measure_labels,
 y_label = "Number of codes for consultations",
 )
 print(plot_conditions)

analysis/reports/pf_report.html

@@ -4,6 +4,7 @@
 #' 
 #' @param data A dataframe containing the data to plot.
 #' @param measure_names Strings specifiying the names of measure columns to be plotted.
+#' @param custom_labels Strings specifying the names of legend labels. 
 #' @param title A string specifying the title of the plot. Default is NULL. 
 #' @param x_label A string specifying the label for the x-axis. Default is NULL.
 #' @param y_label A string specifying the label for the y-axis. Default is NULL. 
@@ -18,6 +19,7 @@
 plot_measures <- function(
     data,
     measure_names,
+    custom_labels = NULL,
     date_col = "interval_end",
     value_col = "numerator",
     measure_col = "measure",
@@ -49,6 +51,12 @@ plot_measures <- function(
   data <- data %>%
     filter(!!measure_sym %in% measure_names)
 
+  # Apply custom labels if provided
+  if (!is.null(custom_labels)) {
+    data <- data %>%
+      mutate(!!measure_sym := factor(!!measure_sym, levels = measure_names, labels = custom_labels))
+  }
+
   # Create plot
   plot1 <- ggplot(
     data,
@@ -66,6 +74,8 @@ plot_measures <- function(
       y = y_label,
       color = color_label
     ) +
+    geom_point() +
+    geom_line(alpha = .5) +
     scale_y_continuous(
       limits = c(0, NA),
     ) +