R/volcono_plot.R

In jaspershen/massstat: Statistical analysis for LC-MS-based metabolomics data

#' #' @title volcano_plot
#' #' @description Draw volcano plot.
#' #' @author Xiaotao Shen
#' #' \email{shenxt1990@@outlook.com}
#' #' @param object tidymass-class object.
#' #' @param fc_column_name fc_column_name
#' #' @param p_value_column_name p_value_column_name
#' #' @param labs_x labs_x
#' #' @param labs_y labs_y
#' #' @param fc_up_cutoff fc_up_cutoff
#' #' @param fc_down_cutoff fc_down_cutoff
#' #' @param p_value_cutoff p_value_cutoff
#' #' @param line_color line_color
#' #' @param up_color up_color
#' #' @param down_color down_color
#' #' @param no_color no_color
#' #' @param point_size point_size
#' #' @param point_alpha point_alpha
#' #' @param point_size_scale point_size_scale
#' #' @param line_type line_type
#' #' @param add_text add_text
#' #' @param text_for text_for
#' #' @param text_from text_from
#' #' @return ggplot2 object
#' #' @export
#' #' @examples
#' #' library(massdataset)
#' #' library(magrittr)
#' #' library(dplyr)
#' #'
#' #' data("liver_aging_pos")
#' #' liver_aging_pos
#' #'
#' #' w_78 =
#' #'   liver_aging_pos %>%
#' #'   activate_mass_dataset(what = "sample_info") %>%
#' #'   dplyr::filter(group == "78W") %>%
#' #'   dplyr::pull(sample_id)
#' #'
#' #' w_24 =
#' #'   liver_aging_pos %>%
#' #'   activate_mass_dataset(what = "sample_info") %>%
#' #'   dplyr::filter(group == "24W") %>%
#' #'   dplyr::pull(sample_id)
#' #'
#' #' control_sample_id = w_24
#' #' case_sample_id = w_78
#' #'
#' #' liver_aging_pos =
#' #'   mutate_fc(
#' #'     object = liver_aging_pos,
#' #'     control_sample_id = control_sample_id,
#' #'     case_sample_id = case_sample_id,
#' #'     mean_median = "mean"
#' #'   )
#' #'
#' #' liver_aging_pos =
#' #'   mutate_p_value(
#' #'     object = liver_aging_pos,
#' #'     control_sample_id = control_sample_id,
#' #'     case_sample_id = case_sample_id,
#' #'     method = "t.test",
#' #'     p_adjust_methods = "BH"
#' #'   )
#' #'
#' #' object = liver_aging_pos
#' #'
#' #' volcano_plot(
#' #'   object = object,
#' #'   fc_column_name = "fc",
#' #'   p_value_column_name = "p_value_adjust",
#' #'   labs_x = "log2(Fold change)",
#' #'   labs_y = "-log(p-adjust, 10)",
#' #'   fc_up_cutoff = 2,
#' #'   fc_down_cutoff = 0.5,
#' #'   p_value_cutoff = 0.05,
#' #'   add_text = TRUE
#' #' )
#' #'
#' #'
#' #' volcano_plot(
#' #'   object = object,
#' #'   fc_column_name = "fc",
#' #'   p_value_column_name = "p_value",
#' #'   labs_x = "log2(Fold change)",
#' #'   labs_y = "-log(p-value, 10)",
#' #'   fc_up_cutoff = 2,
#' #'   fc_down_cutoff = 0.5,
#' #'   p_value_cutoff = 0.05,
#' #'   add_text = FALSE,
#' #'   point_alpha = 0.5
#' #' )
#' #'
#' #' volcano_plot(
#' #'   object = object,
#' #'   fc_column_name = "fc",
#' #'   p_value_column_name = "p_value",
#' #'   labs_x = "log2(Fold change)",
#' #'   labs_y = "-log(p-value, 10)",
#' #'   fc_up_cutoff = 2,
#' #'   fc_down_cutoff = 0.5,
#' #'   p_value_cutoff = 0.05,
#' #'   add_text = FALSE,
#' #'   point_alpha = 0.5,
#' #'   point_size_scale = "p_value"
#' #' ) +
#' #'   scale_size_continuous(range = c(0.5, 3))
#' 
#' volcano_plot <-
#'   function(object,
#'            fc_column_name = "fc",
#'            p_value_column_name = "p_value_adjust",
#'            labs_x = "log2(Fold change)",
#'            labs_y = "-log(p-adjust, 10)",
#'            fc_up_cutoff = 2,
#'            fc_down_cutoff = 0.5,
#'            p_value_cutoff = 0.05,
#'            line_color = "red",
#'            up_color = "#EE0000FF",
#'            down_color = "#3B4992FF",
#'            no_color = "#808180FF",
#'            point_size = 2,
#'            point_alpha = 1,
#'            point_size_scale,
#'            line_type = 1,
#'            add_text = FALSE,
#'            text_for = c("marker", "UP", "DOWM"),
#'            text_from = "variable_id") {
#'     text_for = match.arg(text_for)
#'     massdataset::check_object_class(object = object, class = "mass_dataset")
#'     
#'     if (all(colnames(object@variable_info) != fc_column_name)) {
#'       stop(paste("no", fc_column_name, "in variable_info.\n"))
#'     }
#'     
#'     if (all(colnames(object@variable_info) != p_value_column_name)) {
#'       stop(paste("no", p_value_column_name, "in variable_info.\n"))
#'     }
#'     
#'     variable_info =
#'       object@variable_info
#'     
#'     if (nrow(object@annotation_table) != 0) {
#'       annotation_table =
#'         object@annotation_table %>%
#'         dplyr::group_by(variable_id) %>%
#'         dplyr::slice_head(n = 1) %>%
#'         dplyr::ungroup()
#'       
#'       variable_info =
#'         variable_info %>%
#'         dplyr::left_join(annotation_table %>%
#'                            dplyr::select(-c(ms2_files_id:ms2_spectrum_id)),
#'                          by = "variable_id")
#'     }
#'     
#'     variable_info =
#'       variable_info %>%
#'       dplyr::mutate(log2_fc = log(get(fc_column_name), 2)) %>%
#'       dplyr::mutate(log10_p = -log(get(p_value_column_name), 10)) %>%
#'       dplyr::mutate(
#'         marker = case_when(
#'           log2_fc > log(fc_up_cutoff, 2) &
#'             log10_p > -log(p_value_cutoff, 10) ~ "UP",
#'           log2_fc < log(fc_down_cutoff, 2) &
#'             log10_p > -log(p_value_cutoff, 10) ~ "DOWN",
#'           TRUE ~ "NO"
#'         )
#'       )
#'     
#'     plot =
#'       variable_info %>%
#'       ggplot(aes(log2_fc, log10_p)) +
#'       theme_bw() +
#'       labs(x = labs_x, y = labs_y) +
#'       theme(panel.grid.major = element_blank()) +
#'       geom_vline(
#'         xintercept = log(fc_up_cutoff, 2),
#'         color = line_color,
#'         linetype = line_type
#'       ) +
#'       geom_vline(
#'         xintercept = log(fc_down_cutoff, 2),
#'         color = line_color,
#'         linetype = line_type
#'       ) +
#'       geom_hline(
#'         yintercept = -log(p_value_cutoff, 10),
#'         color = line_color,
#'         linetype = line_type
#'       )
#'     
#'     
#'     if (!missing(point_size_scale)) {
#'       if (all(colnames(object@variable_info) != point_size_scale)) {
#'         stop(paste("no", point_size_scale, "in variable_info.\n"))
#'       } else{
#'         if (length(grep("p_value", point_size_scale)) > 0) {
#'           point_size_scale = "log10_p"
#'         }
#'         plot =
#'           plot +
#'           geom_point(aes(color = marker,
#'                          size = get(point_size_scale)),
#'                      alpha = point_alpha) +
#'           scale_color_manual(values = c(
#'             "UP" = up_color,
#'             "DOWN" = down_color,
#'             "NO" = no_color
#'           )) +
#'           guides(size = guide_legend(title = point_size_scale))
#'       }
#'     } else{
#'       plot =
#'         plot +
#'         geom_point(aes(color = marker),
#'                    size = point_size,
#'                    alpha = point_alpha) +
#'         scale_color_manual(values = c(
#'           "UP" = up_color,
#'           "DOWN" = down_color,
#'           "NO" = no_color
#'         ))
#'     }
#'     
#'     
#'     if (add_text) {
#'       if (all(colnames(variable_info) != text_from)) {
#'         stop(paste("no", text_from, "in variable_info.\n"))
#'       }
#'       
#'       if (text_for == "marker") {
#'         text_data =
#'           variable_info %>%
#'           dplyr::filter(marker %in% c("UP", "DOWN"))
#'       } else{
#'         text_data =
#'           variable_info %>%
#'           dplyr::filter(marker %in% text_for)
#'       }
#'       
#'       
#'       if (requireNamespace("ggrepel", quietly = TRUE)) {
#'         plot =
#'           plot +
#'           ggrepel::geom_text_repel(aes(log2_fc, log10_p,
#'                                        label = get(text_from)),
#'                                    data = text_data)
#'       } else{
#'         message("Please install ggrepel package first.")
#'       }
#'       
#'     }
#'     
#'     return(plot)
#'   }