ComplexUpset with icons

upset_with_icons.R

# for indvs and symptoms see https://github.com/kjhealy/covid_symptoms
mapping = list(
    'Fatigue'='tired-regular',
    'Anosmia'='socks-solid',
    'Cough'='head-side-cough-solid',
    'Fever'='thermometer-full-solid',
    'Diarrhea'='toilet-solid',
    'Breath'='lungs-solid'
)

map_to_icon = function(x) {
    # download from https://fontawesome.com/
    paste0("<img src='archive/font-awesome-icons/", mapping[x], ".png'>")
}

patchwork::wrap_elements(
    patchwork::wrap_elements(
        upset(
            indvs, symptoms,
            name="Symptom Groupings by Frequency. Total pool is 1,764 individuals. Combinations with <10 not shown,",
            min_size = 10,
            width_ratio = 0.125,
            labeller=map_to_icon,
            queries=list(
                upset_query(
                    set='Anosmia',
                    fill='red',
                    only_components=c('overall_sizes')
                ),
                upset_query(
                    intersect=c('Fatigue', 'Fever', 'Cough'),
                    fill='blue', color='blue'
                )
            )
        )
        + labs(
            title = "Co-Occurence of COVID-19 Symptoms",
            caption = "Data: covid.joinzoe.com/us | Graph: @kjhealy + @krassowski | Icons: FontAwesome CC BY 4.0"
        )
        + theme(
            axis.text.y = ggtext::element_markdown(color = "black", size = 11, hjust = 0.5)
        )
    )
    + (
        ggplot(data.frame(symptom=symptoms), aes(y=symptom))
        + ggtext::geom_richtext(
            aes(label=map_to_icon(symptoms)),
            x=0.15,
            label.color=NA
        )
        + ggtext::geom_richtext(
            aes(label=symptom),
            x=0.3,
            hjust=0,
            label.color=NA
        )
        + xlim(0, 1.5)
        + theme_void()
        + ggtitle('Symptoms')
    )
    + patchwork::plot_layout(design=c(
        patchwork::area(t=1, l=1, b=12, r=60),
        patchwork::area(t=2, l=2, b=5, r=8)
    ))
) + labs(
    title='Loss of smell (anosmia, in red) was highlighted as a strong predictor of COVID-19 infection in a recent preprint by (Menni, et al, 2020)',
    subtitle='Having all three "frequent" symptoms (according to WHO, as per 2020-04-16) is rare (blue)'
)