# Pie-chart lollipop plots

This example shows the use of `PieGlyph` package to create lollipop plots where the centre of the lollipop is replaced by a pie-chart showing proportion of different attributes.

This examples highlights that proportions or percentages are not required for the attribute values in the raw data; the package will take counts or other attribute values and automatically convert them to proportions to generate the graph. Further, the attributes don’t always have to be in separate columns, they can also be stacked in one column with their corresponding values in another column.

### Load libraries

    library(PieGlyph)
    library(ggplot2)
    library(forcats)
    library(dplyr)
    library(tidyr)

### Create fake data

    model_data <- data.frame('ID' = paste0('P', 1:20),
                             'A' = c(90, 60, 30, 75, 85,
                                     30, 50, 70, 65, 65,
                                     40, 115, 165, 40, 175,
                                     200, 185, 250, 190, 175),
                             'B' = c(170, 180, 130, 325, 180,
                                     220, 335, 285, 85, 125,
                                     250, 190, 60, 205, 125,
                                     90, 95, 25, 60, 20),
                             'C' = c(60, 35, 95, 50, 15,
                                     190, 15, 80, 310, 280,
                                     185, 115, 220, 190, 155,
                                     135, 180, 120, 100, 140),
                             'D' = c(180, 225, 245, 50, 220,
                                     60, 100, 65, 40, 30,
                                     25, 80, 55, 65, 45,
                                     75, 30, 105, 150, 165),
                             'Disease' = factor(c(rep(c('Yes'), 10),
                                                  rep(c('No'), 10))))

The data contains proportions of four protein markers in the blood for 20 different patients. `ID` is a unique identifier for each patients while columns `A`, `B`, `C`, and `D` describe the scores of each patient across the four markers and `disease` describes whether of not the patient has a disease.

    head(model_data)
    #>   ID  A   B   C   D Disease
    #> 1 P1 90 170  60 180     Yes
    #> 2 P2 60 180  35 225     Yes
    #> 3 P3 30 130  95 245     Yes
    #> 4 P4 75 325  50  50     Yes
    #> 5 P5 85 180  15 220     Yes
    #> 6 P6 30 220 190  60     Yes

### Fit logistic regression model

We fit a logistic regression model with no intercept using the four protein markers as predictors for the probability of having the disease.

    m1 <- glm(Disease ~ 0 + A + B + C + D,
              data = model_data,
              family = binomial(link = 'logit'))

The model summary shows that marker `A` is significant in predicting the probability of having the disease.

    summary(m1)
    #>
    #> Call:
    #> glm(formula = Disease ~ 0 + A + B + C + D, family = binomial(link = "logit"),
    #>     data = model_data)
    #>
    #> Coefficients:
    #>    Estimate Std. Error z value Pr(>|z|)
    #> A -0.035561   0.018041  -1.971   0.0487 *
    #> B  0.005089   0.004897   1.039   0.2987
    #> C  0.003451   0.005785   0.597   0.5508
    #> D  0.022697   0.015913   1.426   0.1538
    #> ---
    #> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    #>
    #> (Dispersion parameter for binomial family taken to be 1)
    #>
    #>     Null deviance: 27.726  on 20  degrees of freedom
    #> Residual deviance: 13.221  on 16  degrees of freedom
    #> AIC: 21.221
    #>
    #> Number of Fisher Scoring iterations: 6

### Model predictions

We can now predict the probability of a patient having the disease give their scores on the four protein markers.

After making the predictions, the data is sorted in descending order of the probability of having the disease. Further the marker columns are stacked together into one column.

    plot_data <- model_data %>%
      # Add predictions
      mutate('prediction' = predict(m1, type = 'response')) %>%
      # Sort in descending order of prediction
      arrange(desc(prediction)) %>%
      # Relevel ID for plotting in descending order
      mutate(ID = fct_inorder(ID)) %>%
      # Stack the four markers in one column
      pivot_longer(cols = c('A', 'B', 'C','D'), names_to = 'Marker',
                   values_to = 'Proportion')

    head(plot_data, 8)
    #> # A tibble: 8 × 5
    #>   ID    Disease prediction Marker Proportion
    #>   <fct> <fct>        <dbl> <chr>       <dbl>
    #> 1 P3    Yes          0.996 A              30
    #> 2 P3    Yes          0.996 B             130
    #> 3 P3    Yes          0.996 C              95
    #> 4 P3    Yes          0.996 D             245
    #> 5 P2    Yes          0.982 A              60
    #> 6 P2    Yes          0.982 B             180
    #> 7 P2    Yes          0.982 C              35
    #> 8 P2    Yes          0.982 D             225

### Bar plot

The probability of each patient in our sample having the disease can be visualised with a bar chart as follows.

    # Filtering the data as each prediction is replicated 4 times, once for each marker
    ggplot(data = filter(plot_data, Marker == 'A'))+
      geom_col(aes(x = ID, y = prediction))+
      # Add axis titles
      labs(y = 'Prob(Having Disease)', x = 'Patient')+
      theme_minimal()

### Lollipop plot with pie-charts

The bar plot is not that useful in this example as it gives only the probability of having the disease and gives no information about the model predictors (scores for protein markers in this case).

We can improve this plot by converting it into a lollipop plot where the centre of the lollipop shows the proportions of the four protein markers. This enables us to view both, the response as well as the predictors for model simultaneously.

    ggplot(data = plot_data, aes(x = ID, y = prediction, fill = Marker))+
      # Vertical line of lollipop
      geom_segment(aes(yend = 0, xend = ID))+
      # Pies-charts at the centre of the lollipop
      geom_pie_glyph(slices = 'Marker', values = 'Proportion',
                     radius = 0.3, colour = 'black')+
      # Axis titles
      labs(y = 'Prob(Having Disease)', x = 'Patient')+
      # Colours for sectors of the pie-chart
      scale_fill_manual(values = c('#56B4E9','#F0E442',
                                   '#D55E00','#CC79A7'))+
      theme_minimal()