inst/Kronos_scRT_tools/R/scCN.R

In Derfen3001/Kronos.scRT: R-package and Shiny App interface for the analysis of single cell replication timing data

scCN_ui <- function(id, title = NULL) {
  ns <- shiny::NS(id)
  shinydashboard::box(
    id = ns('box'),
    status = 'primary',
    title = title,
    width = 12,
    solidHeader = T,
    collapsible = T,
    shiny::fluidRow(plotOutput(
      ns('plot__scCN'), height = "auto", width = '60%'
    ), align = 'center')
  )
}


scCN_server <-
  function(id,
           S_Traks,
           G_Traks,
           Levels = 10,
           out,
           save,
           size_plot) {
    shiny::moduleServer(id,
                        function(input,
                                 output,
                                 session,
                                 S = S_Traks,
                                 G = G_Traks,
                                 L = Levels,
                                 Out = out,
                                 Save = save,
                                 plot_size = size_plot,
                                 ID = id) {
                          #load required operators
                          `%>%` = tidyr::`%>%`

                          tracks = tryCatch(
                            rbind(
                              G %>% dplyr::select(chr, start, end, CN, newIndex, group) %>%
                                dplyr::mutate(phase = 'G1G2-phase') %>%
                                dplyr::ungroup(),
                              S %>% dplyr::select(chr, start, end, CN, newIndex, group) %>%
                                dplyr::mutate(phase = 'S-phase') %>%
                                dplyr::ungroup()
                            ),
                            error = function(x)
                              dplyr::tibble()

                          )

                          if (nrow(tracks) != 0) {
                            tracks = tracks %>% dplyr::mutate(
                              CN = round(CN),
                              MaxAllowed = min(CN, na.rm = T) +
                                L,
                              CN = ifelse(CN > MaxAllowed, MaxAllowed, CN)
                            ) %>%
                              dplyr::arrange(CN) %>%
                              dplyr::mutate(CN = factor(CN)) %>%
                              tidyr::drop_na() %>%
                              dplyr::arrange(chr, start)

                            Chr = unique(tracks$chr)

                            plot =
                              ggplot2::ggplot() +
                              ggplot2::geom_rect(
                                data = tracks ,
                                ggplot2::aes(
                                  xmin = start,
                                  xmax = end,
                                  ymin = -newIndex,
                                  ymax = -newIndex - 1,
                                  fill = CN
                                )
                              ) + ggplot2::facet_grid(phase ~ ., scales = 'free_y', space =  'free_y') +
                              ggplot2::scale_x_continuous(
                                labels = function(x)
                                  paste(x / 10 ^ 6, 'Mb', sep = ' ')
                              ) + ggplot2::theme(
                                legend.position = 'right',
                                legend.direction = "vertical",
                                axis.text.y = ggplot2::element_blank(),
                                axis.ticks.y = ggplot2::element_blank(),
                                axis.text.x = ggplot2::element_text(
                                  angle = 45,
                                  hjust = 1,
                                  vjust = 1
                                )

                              ) +
                              ggplot2::xlab(Chr) +
                              ggplot2::scale_fill_manual(values = viridis::viridis(L +
                                                                                     1))

                          } else{
                            plot = ggplot2::ggplot()

                          }
                          output$plot__scCN <- renderPlot({
                            plot
                          },
                          height = function() {
                            session$clientData[[paste0('output_', ID, '-plot__scCN_width')]] * plot_size$height / plot_size$width
                          })
                          #save
                          if (Save) {
                            start = min(tracks$start) / 10 ^ 6
                            end = max(tracks$end) / 10 ^ 6
                            group = unique(tracks$group)
                            Chr = unique(tracks$chr)

                            ggplot2::ggsave(
                              plot = plot,
                              filename = file.path(
                                Out,
                                paste0(group, '_', Chr, '_', start, 'Mb_', end, 'Mb.pdf')
                              ),
                              device = grDevices::cairo_pdf,
                              width = plot_size$width,
                              height = plot_size$height,
                              units = plot_size$unit
                            )
                          }

                        })
  }