---
title:      'Visualize the impact of changing definitions of HiSCR response on the results'
author:     Agustin Calatroni 
date:       "`r format(Sys.Date(), format='%a %d %b %Y')`" 
output: 
   flexdashboard::flex_dashboard:
     orientation: columns
     self_contained: true
     source_code: "https://github.com/agstn/WW/tree/main/2022-04-13"
---

```{=html}
<style type="text/css">
.main-container {
max-width:    1200px;
margin-left:  auto;
margin-right: auto;}
.rt-compact .rt-td-inner{
padding: 0px 6px;
}
</style>
```

```{r knitr-defaults}
knitr::opts_chunk$set(warning = FALSE, message = FALSE, comment = NA)
knitr::opts_chunk$set(cache = FALSE)
options(width=170)
```

```{r load-packages}
pacman::p_load(tidyverse, rio)
pacman::p_load(reactable, reactablefmtr, plotly)
pacman::p_load(htmltools, htmlwidgets, crosstalk)
```

```{r import-data}
#https://themockup.blog/posts/2020-05-29-client-side-interactivity-do-more-with-crosstalk/
#https://github.com/kcuilla/2020-RStudio-Table-Contest-Entry2

dd_mod <- rio::import('dat/HiSCR_dat_mod.rds') %>% 
   select(an.count, abscesses, drain.fist, n_y, 
          p_a:p_l10) 

dd_cross <- SharedData$new(dd_mod)
```

# Definitions

Inputs {.sidebar data-width=250}
--------------------------------------------------

A patient reaches a **HiSCR response**, if all of the following three conditions are met, when the baseline data are compared to the follow-up data (at week 16):

**at least a XX% decrease in (AN) count** <br>
AN count is defined as the sum of the number of abscess and the number of inflammatory nodules

```{r input-filters-1}
filter_slider(
   id = "an.count",
   #label = "% (AN) count decrease",
   label = NULL,
   sharedData = dd_cross,
   column = ~ an.count,
   ticks = TRUE,
   post = '%',
   step = 25,
   width = "75%")
```

**XX decrease in the number of abscesses**

```{r input-filters-2}
filter_slider(
   id = "abscesses",  
   #label = "decrease # abscesses", 
   label = NULL,
   sharedData = dd_cross,
   pre = '#',
   column = ~abscesses, 
   step = 1,
   width = "75%")
```

**XX decrease in the number of draining fistulae**

```{r input-filters-3}
filter_slider(
   id = "drain.fist",  
   #label = "decrease # daining fistulae", 
   label = NULL,
   sharedData = dd_cross,
   pre = '#',
   column = ~drain.fist, 
   step = 1,
   width = "75%")
```

Column
--------------------------------------------------

### VOLCANO PLOT {data-height=825}

```{r figure-plotly}
g1 <- ggplot(data = dd_cross,
             aes(x = d_n, 
                 y = p_l10,
                 size = n_y,
                 alpha = 0.5,
                 text = paste('Difference (95%CI)',   d_e, d_c,
                              '<br> -log10(p)=', round(p_l10,2), '& p:', d_f,
                              '<br> HiSCR (Yes):', n_y))) +
   geom_vline(xintercept = 0,            col = 'gray50') +
   geom_hline(yintercept = -log10(0.05), col = 'gray50') +
   geom_point() +
   scale_alpha_identity() +
   scale_x_continuous(name = 'Difference<br>(Active-Placebo)',
                      limits = c(-15, 40),
                      breaks = c(-10, -5, 0, 5, 10, 20, 30, 40)) +
   scale_y_continuous(name = '-log10(p-value)',
                      expand = c(0.02, 0.02),
                      limits = c(0, 15),
                      breaks = c(0,    1.3,             4.6,             5,    6.9,                 10,   15),
                      labels = c('0', '1.3\n(p=0.05)', '\n 4.6\n(p=0.01)', '5\n','6.9\n(p=0.001)', '10', '15'),
                      sec.axis = sec_axis( trans=~ 1/(10^(.)),
                                           breaks = c(0.99,     0.5,   0.05,  0.01,    0.001,   0.0001),
                                           labels = c('>0.99', '0.5', '0.05', '0.01', '0.001', '0.0001'),
                                           name="p-value")
   ) +
   theme_bw()


ggplotly(g1,
         tooltip = c("text"),
         width  = 685,
         height = 650) %>% 
   add_text(
      x = ~32, y = ~14.34,
      text = ~"HiSCR-Original Def.",
      showlegend = FALSE, hoverinfo = "none",
      color = I("black"), size = I(9)
   ) %>% 
   layout(
    xaxis = list(fixedrange = TRUE),
    yaxis = list(fixedrange = TRUE)
  )
```


### ORIGINAL DEFINITION RESULTS {data-height=175}

```{r table-gtsummary}
pacman::p_load(gtsummary)

dd_w <- rio::import('dat/HiSCR_dat_w.rds') 

theme_gtsummary_compact()

dd_w %>% 
   tbl_summary(by      = TRT,
               include = HiSCR ,
               label = list(HiSCR ~ 
                               "<=50% (AN) count +  
                              #0 abscesses +
                              #0 draining fistulae"),
               statistic = all_categorical(dichotomous = TRUE) ~ "{p}% ({n})") %>% 
   add_difference(pvalue_fun = ~style_ratio(-log10(.x), digits = 3)) %>% 
   modify_cols_merge(pattern = "<b>{estimate}</b> <br><small>({ci})</small>") %>% 
   modify_header(estimate  = "Difference <br><small>(95% CI)</small>",
                 label     = "HiSCR-Original (Yes)",
                 p.value   = "-log10(p-value)",
                 all_stat_cols() ~ "{level} <br><small>N = {n}</small>",
                 text_interpret = 'html') %>%
   modify_footnote(update = everything() ~ NA)
```

Column
--------------------------------------------------

### RESULTS TABLE 

```{r table-reactable}
reactable( 
   dd_cross,
   theme = fivethirtyeight(centered = TRUE, header_font_size = 12),
   pagination   = FALSE,
   showSortIcon = FALSE,
   highlight = TRUE,
   # compact      = TRUE,
   # height       = 800, 
   selection = "multiple", onClick = "select",
   defaultSorted = list(p_l10 = "desc"),
   columnGroups = list(
      colGroup(name = "definition of HiSCR response", columns = c("an.count", "abscesses","drain.fist")),
      colGroup(name = "Two-Sample Proportions Test", columns = c("p_a","n_a","p_p","n_p","d_e","d_f","p_l10"))
   ),
   defaultColDef = colDef(align = 'right',
                          sortable = FALSE),
   columns = list(
      d_l = colDef(show = F),
      d_u = colDef(show = F),
      an.count = colDef(show = T,
                        sortable = TRUE,
                        name = 'AN Count',
                        maxWidth = 65),
      abscesses = colDef(show = T,
                         sortable = TRUE,
                         name = 'draining fistulae',
                         maxWidth = 65),
      drain.fist = colDef(show = T,
                          sortable = TRUE,
                          name = 'abscesses',
                          maxWidth = 75),
      p_a = colDef(name = 'Active <br><small>N = 200</small>',
                   html = TRUE,
                   maxWidth = 70,
                   format = colFormat(suffix = '%',
                                      digits = 1),
                   cell = merge_column(dd_mod, "n_a")
      ),
      n_a = colDef(show = F),
      p_p = colDef(name = 'Placebo <br><small>N = 200</small>',
                   html = TRUE,
                   maxWidth = 70,
                   format = colFormat(suffix = '%',
                                      digits = 1),
                   cell = merge_column(dd_mod, "n_p")),
      n_p = colDef(show = F),
      
      d_e = colDef(name = 'Difference (95%CI)<br><small>(Active-Placebo)</small>',
                   html = TRUE,
                   align = 'right',
                   cell = merge_column(dd_mod, "d_c"),
                   width = 125),
      
      n_y = colDef(show = F),
      d_n = colDef(show = F),
      d_c = colDef(show = F),
      d_l = colDef(show = F),
      d_u = colDef(show = F),
      
      p_l10 = colDef(name = "UNADJ <br><small>-log10(p-value)</small>",
                     sortable = TRUE,
                     maxWidth = 65,
                     html = TRUE,
                     format = colFormat(digits = 2)),
      
      p_n   = colDef(show = F,
                     name = "UNADJ <br>p-value",
                     html = TRUE,
                     format = colFormat(digits = 3)),
      
      d_f   = colDef(name = "UNADJ <br><small>p-value</small>",
                     maxWidth = 65,
                     html = TRUE,
                     align = 'right')
   )
)
```