R/functions_OLD.R

In tidygate: Interactively Gate Points

#' @importFrom rlang quo_is_symbol
#' @importFrom grDevices colorRampPalette
#' @importFrom RColorBrewer brewer.pal
#' @importFrom viridis viridis
#' @import dplyr
#' @import tidyr
#' @importFrom scales rescale
#' @importFrom rlang :=
#' @importFrom graphics axis
#' @importFrom graphics legend
#' @importFrom graphics par
#' @importFrom utils head
#' @importFrom stringr str_pad
#' @importFrom scales alpha

pretty_plot = function(.data,
                       .dim1,
                       .dim2,
                       .color=NULL,
                       .shape=NULL,
                       .size=NULL,
                       opacity = 1){
  
  # Comply with CRAN NOTES
  . = NULL
  
  # Get column names
  .dim1 = enquo(.dim1)
  .dim2 = enquo(.dim2)
  .color = enquo(.color)
  .shape = enquo(.shape)
  
  my_size_range = c(1,3)
  
  
  
  .data_formatted = 
    .data %>%
    
    # Define COLOR
    when(
      
      # If continuous
      quo_is_symbol(.color) && 
        (.) %>% 
        select(!!.color) %>% 
        sapply(class) %in% c("numeric", "integer", "double") ~{
          order_ = findInterval( pull(.,!!.color), sort(pull(.,!!.color)))
          (.) %>% mutate(.color = grDevices::colorRampPalette(	viridis(n = 5) )(n())[order_] )
        },
      
      # If discrete
      quo_is_symbol(.color) ~ {
        how_many_colors = .data %>% distinct(!!.color) %>% nrow
        (.) %>%
          mutate(.color = 
                   grDevices::colorRampPalette(RColorBrewer::brewer.pal(min(9, how_many_colors), "Set1"))(how_many_colors)[factor(!!.color)]
          )
      },
      
      # If not defined
      ~ (.) %>% mutate(.color = "grey25")
    ) %>%
    
    # Define SIZE
    when(
      
      # If not defined
      is.null(.size) ~ (.)  %>% mutate(.size = 2 ),
      
      # If it is a number and not a column name
      .size %>% is("numeric") ~ (.)  %>% mutate(.size := !!.size ),
      
      # If continuous
      quo_is_symbol(enquo(.size)) && 
        (.) %>% 
        select(!!enquo(.size)) %>% 
        sapply(class) %in% c("numeric", "integer", "double") ~ 	(.) %>%	mutate(.size := !!enquo(.size) %>% rescale( to = my_size_range) ),
      
      # If discrete
      quo_is_symbol(enquo(.size)) ~ {
        warning("tidygate says: .size has to be a continuous variable. .size has been ignored")
        (.) %>% mutate(.size = 2 )
      },
      
      ~ stop("tidygate says: the parameter .size must be NULL, numeric or a symbolic column name")
    ) %>%
    
    # Define SHAPE
    when(
      
      # If continuous
      quo_is_symbol(.shape) & 
        (.) %>% 
        select(!!.shape) %>% 
        sapply(class) %in% c("numeric", "integer", "double") ~ {
          warning("tidygate says: .shape has to be a discrete variable. .shape has been ignored")
          (.) %>% mutate(.shape = 19 )
        }	,
      
      # If discrete
      quo_is_symbol(.shape) ~ (.) %>%	mutate(.shape := c(19, 17, 15, 18, 3, 4, 8, 10, 5)[factor(!!.shape)] 	),
      
      # If not defined
      ~ (.)  %>% mutate(.shape = 19 )
    ) 
  
  # Plot
  .data_formatted %>%
    {
      plot(
        (.) %>% pull(!!.dim1),
        (.) %>% pull(!!.dim2),
        xlim=range((.) %>% pull(!!.dim1)), 
        ylim=range((.) %>% pull(!!.dim2)),
        bty='l',
        pch=(.) %>% pull(.shape),
        cex = (.) %>% pull(.size),
        col=(.) %>% pull(.color) %>% alpha(opacity),
        xlab = quo_names(.dim1) %>% paste(collapse= " "),
        ylab = quo_names(.dim2) %>% paste(collapse= " "),
        xaxt='n',
        yaxt='n'
      )
    }
  
  axis(1, tck=1,  col.ticks="light gray")
  axis(1, tck=-0.015, col.ticks="black", labels = FALSE)
  axis(2, tck=1,  col.ticks="light gray", lwd.ticks="1", las=1)
  axis(2, tck=-0.015, col.ticks="black", las=1, labels = FALSE)
  
  # Max length of the legends titles
  color_title = quo_name(.color)
  shape_title = quo_name(.shape)
  size_title = quo_name(.size)
  max_length_titles = max(nchar(color_title), nchar(shape_title), nchar(size_title))
  color_title = stringr::str_pad(color_title, width = max_length_titles, side = "both")
  shape_title = stringr::str_pad(shape_title, width = max_length_titles, side = "both")
  size_title = stringr::str_pad(size_title, width = max_length_titles, side = "both")
  
  # Add legend to top right, outside plot region
  inset_y = 0
  if(	quo_is_symbol(.color)){
    legend(
      "topleft", 
      inset=c(1.05,inset_y),
      legend=distinct(.data_formatted, !!.color) %>% pull(!!.color),
      pch=19, 
      col = distinct(.data_formatted, !!.color, .color) %>% pull(.color),
      title=color_title, 
      box.col="white",
      xjust = 0
    )
    inset_y = inset_y + distinct(.data_formatted, !!.color, .color) %>% nrow %>% magrittr::multiply_by(.1)
  }
  if(	quo_is_symbol(enquo(.size)) && (.data %>% select(!!enquo(.size)) %>% sapply(class) %in% c("numeric", "integer", "double") )){
    legend(
      "topleft",
      inset=c(1.05,inset_y),
      legend=distinct(.data_formatted, !!enquo(.size)) %>% pull(!!enquo(.size)) %>% range,
      pch=19,
      col = "black",
      pt.cex = my_size_range,
      title=size_title,
      box.col="white",
      xjust = 0
    )
    inset_y = inset_y + 0.3
  }
  if(	quo_is_symbol(.shape)){
    legend(
      "topleft", 
      inset=c(1.05,inset_y),
      legend=distinct(.data_formatted, !!.shape) %>% pull(!!.shape),
      pch=distinct(.data_formatted, !!.shape, .shape) %>% pull(.shape), 
      col = "black",
      title=shape_title, 
      box.col="white",
      yjust = 0
    )
    inset_y = inset_y + distinct(.data_formatted, !!.shape, .shape) %>% nrow %>% magrittr::multiply_by(.1)
  }
  
  
  
}

#' Get points within a user drawn gate
#' 
#' @keywords internal
#'
#' @import dplyr
#' @import tidyr
#' @import tibble
#' @importFrom graphics plot
#' @importFrom purrr imap
#' @importFrom purrr map
#'
#' @param .data A tibble
#' @param .element A column symbol. The column that is used to calculate distance (i.e., normally genes)
#' @param .dim1 A column symbol. The x dimension
#' @param .dim2 A column symbol. The y dimension
#' @param .color A column symbol. Color of points
#' @param .shape A column symbol. Shape of points
#' @param .size A column symbol. Size of points
#' @param opacity A number between 0 and 1. The opacity level of the data points
#' @param  how_many_gates An integer. The number of gates to label
#' @param name A character string. The name of the new column
#' @param ... Further parameters passed to the function gatepoints::fhs
#'
#' @return A tibble with additional columns
#'
gate_interactive_old <-
  function(.data,
           .element,
           .dim1,
           .dim2, 
           .color = NULL,
           .shape = NULL,
           .size = NULL,
           opacity = 1,
           how_many_gates = 1,
           name = "gate", ...) {
    
    # Comply with CRAN NOTES
    . = NULL
    value = NULL
    
    # Get column names
    .element = enquo(.element)
    .dim1 = enquo(.dim1)
    .dim2 = enquo(.dim2)
    .color = enquo(.color)
    .shape = enquo(.shape)
    
    
    # Error if elements with coordinates are not unique
    .data %>% check_data_unique(!!.element,  !!.dim1, !!.dim2)
    
    # my df
    my_df = 
      .data %>%
      select(!!.element, get_specific_annotation_columns(.data, !!.element)) %>%
      distinct %>%
      
      # Check if dimensions are NA
      check_dimensions(!!.dim1, !!.dim2) 
    
    my_matrix	=
      my_df %>%
      select(!!.element, !!.dim1, !!.dim2) %>%
      .as_matrix(rownames = !!.element) 
    
    # Add extra space to right of plot area; change clipping to figure
    if(
      quo_is_symbol(.color) | 
      quo_is_symbol(.shape) | 
      (quo_is_symbol(enquo(.size))  && (.data %>% select(!!enquo(.size)) %>% sapply(class) %in% c("numeric", "integer", "double")))
    ){
      # Reset par on exit
      opar <- par(no.readonly =TRUE)  
      on.exit(par(opar)) 
      
      # Set the new par
      par(
        mar=c(5.1, 4.1, 4.1, 8.1),
        xpd=TRUE,
        tck = -.01 # Reduce tick length
      )
    }
    
    
    # Plot
    my_df %>% pretty_plot(
      !!.dim1, 
      !!.dim2,
      .color = !!.color,
      .shape = !!.shape,
      
      # size can be number or column
      .size = .size %>% when(is.null(.size) |  is(., "numeric")  ~ (.), ~ !!enquo(.)),
      
      opacity = opacity
    )
    
    # Loop over gates # Variable needed for recalling the attributes later
    gate_list = map(1:how_many_gates,  ~ my_matrix %>% fhs(mark = TRUE, ...))
    
    
    
    # Return
    gate_list %>%
      
      # Format
      imap( ~ .x %>% format_gatepoints(!!.element, name, .y)) %>%
      purrr::reduce(full_join, by = quo_names(.element)) %>%
      unite(col = !!name,
            contains(name),
            sep = ",",
            na.rm = TRUE) %>%
      
      # Correct column types
      # Keep classes for compatibility
      imap(
        ~ .x %>%
          when(
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is("numeric") ~ as.numeric(.),
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is( "integer") ~ as.integer(.),
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is( "logical") ~ as.logical(.),
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is( "factor") ~ as.factor(.),
            ~ (.)
          )
      ) %>%
      do.call(bind_cols, .) %>%
      
      # Join with the dataset
      right_join(my_df %>% select(!!.element),
                 by = quo_names(.element)) %>%
      
      # Replace NAs
      mutate(!!name := replace_na(!!as.symbol(name), "0")) %>%
      
      # Add internals the list of gates
      add_attr(map(gate_list, ~ attr(.x, "gate")), "gate") 
    
  }

#' Get points within a user drawn gate
#' 
#' @keywords internal
#'
#' @import dplyr
#' @import tidyr
#' @import tibble
#' @importFrom graphics plot
#' @importFrom purrr imap
#' @importFrom purrr map
#'
#' @param .data A tibble
#' @param .element A column symbol. The column that is used to calculate distance (i.e., normally genes)
#' @param .dim1 A column symbol. The x dimension
#' @param .dim2 A column symbol. The y dimension
#' @param gate_list A list of gates. Each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.
#' @param name A character string. The name of the new column
#' @param ... Further parameters passed to the function gatepoints::fhs
#'
#' @return A tibble with additional columns
#'
gate_programmatic_old <- 
  function(.data,
           .element,
           .dim1,
           .dim2, 
           gate_list,
           name = "gate", 
           ...) {
    
    # Comply with CRAN NOTES
    . = NULL
    value = NULL
    
    # Get column names
    .element = enquo(.element)
    .dim1 = enquo(.dim1)
    .dim2 = enquo(.dim2)
    
    # Error if elements with coordinates are not unique
    .data %>% check_data_unique(!!.element,  !!.dim1, !!.dim2)
    
    # my df
    my_df = 
      .data %>%
      select(!!.element, get_specific_annotation_columns(.data, !!.element)) %>%
      distinct %>%
      
      # Check if dimensions are NA
      check_dimensions(!!.dim1, !!.dim2) 
    
    my_matrix	=
      my_df %>%
      select(!!.element, !!.dim1, !!.dim2) %>%
      .as_matrix(rownames = !!.element) 
    
    # Loop over gates # Variable needed for recalling the attributes later
    gate_list_result = map(
      gate_list,  
      ~ my_matrix[applyGate(my_matrix,.x),] %>%
        rownames() %>% 
        
        # Avoid error for empty gates
        when(!is.null(.) ~ (.) %>% add_attr(.x, "gate") )
    )
    
    # Return
    gate_list_result %>%
      
      # Format
      imap( ~ .x %>% format_gatepoints(!!.element, name, .y)) %>%
      purrr::reduce(full_join, by = quo_names(.element)) %>%
      unite(col = !!name,
            contains(name),
            sep = ",",
            na.rm = TRUE) %>%
      
      # Correct column types
      # Keep classes for compatibility
      imap(
        ~ .x %>%
          when(
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is("numeric") ~ as.numeric(.),
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is( "integer") ~ as.integer(.),
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is( "logical") ~ as.logical(.),
            .y %in% colnames(my_df) &&
              my_df %>% select(.y) %>% pull(1) %>% is( "factor") ~ as.factor(.),
            ~ (.)
          )
      ) %>%
      do.call(bind_cols, .) %>%
      
      # Join with the dataset
      right_join(my_df %>% select(!!.element),
                 by = quo_names(.element)) %>%
      
      # Replace NAs
      mutate(!!name := replace_na(!!as.symbol(name), "0")) %>%
      
      # Add internals the list of gates
      add_attr(gate_list, "gate") 
    
  }