New Function for DME -- PlotDMEslollipop

   p + NoLegend()

}

#' PlotDMEslollipop

#'

#' Plotting function for the results of FindDMEs and FindAllDMEs

#'

#' @param seurat_obj A Seurat object

#' @param DMEs dataframe output from FindDMEs or FindAllDMEs

#' @param group.by the column name of the selected comparison in the DMEs dataframe

#' @param comparison character vector or a list of character vectors containing the comparison in the DMEs dataframe

#' @param pvalue p_value or fdr used for the comparison in the DMEs dataframe

#' @keywords scRNA-seq

#' @export

#' @return A ggplot object

#' @examples

#' plot_list <- PlotDMEslollipop(seurat_obj, DMEs, group.by = "Comparison", comparison = c("Disease_vs_Control"), pvalue = "p_val_adj")

PlotDMEslollipop <- function(

  seurat_obj,

  DMEs,

  wgcna_name,

  group.by=NULL,

  comparison= NULL,

  pvalue,

  avg_log2FC = 'avg_log2FC'

){

  if (!require("ggforestplot")) {

    print('Missing package: ggforestplot')

    print('Installing package: ggforestplot')

    devtools::install_github("NightingaleHealth/ggforestplot")

  }

  if(!(pvalue %in% colnames(DMEs))){

  stop('Selected pvalue is not found in DMEs dataframe column names.')

  }

  if(missing(wgcna_name) || !(wgcna_name %in% names(seurat_obj@misc))){

  stop('Please provide wgcna_name or the selected wgcna_name is not found in seurat_obj@misc.')

  }

  modules <- GetModules(seurat_obj, wgcna_name) %>% subset(module != 'grey') %>% mutate(module=droplevels(module))

  if (!missing(group.by) & !missing(comparison)) {

    comparisons <- comparison

    if(!(all(comparisons %in% DMEs[[group.by]]))){

    stop('Not all selected comparisons are not found in DMEs[[group.by]] or the comparison column, DMEs[[group.by]], is not correctly supplied.')

    }

    # comparisons <- unique(DMEs$comparison)

    plot_list <- list()

    for(cur_comp in comparisons){

        print(cur_comp)

        # cur_DMEs <- DMEs %>% filter(DMEs[[group.by]] == cur_comp)

        cur_DMEs <- subset(DMEs, DMEs[[group.by]] == cur_comp)

        # provide title

        cur_title <- cur_comp

        #

        p <- Plotlollipop(modules, cur_DMEs, pvalue, avg_log2FC = 'avg_log2FC')

        p <- p + ggtitle(cur_title) + NoLegend() +  ggforestplot::geom_stripes(aes(y=module), inherit.aes=FALSE, data=cur_DMEs)

        plot_list[[cur_comp]] <- p

      }

  } else if (missing(group.by) && !missing(comparison)) { # Using && instead of & ensures that the second condition is only evaluated if the first condition is TRUE.

    stop('The group.by column is not provided in the DMEs data, and comparison cannot be found.')

  } else if (!missing(group.by) && missing(comparison)) { # Using && instead of & ensures that the second condition is only evaluated if the first condition is TRUE.

    if (!(group.by %in% names(DMEs))) {

    stop('The group.by column is not found in the DMEs data.')

    }

    comparisons <- unique(DMEs[[group.by]])

    plot_list <- list()

    for(cur_comp in comparisons){

        print(cur_comp)

        # cur_DMEs <- DMEs %>% filter(DMEs[[group.by]] == cur_comp)

        cur_DMEs <- subset(DMEs, DMEs[[group.by]] == cur_comp)

        # provide title

        cur_title <- cur_comp

        # set plotting attributes for shape

        p <- Plotlollipop(modules, cur_DMEs, pvalue, avg_log2FC = 'avg_log2FC')

        p <- p + ggtitle(cur_title) + NoLegend() +  ggforestplot::geom_stripes(aes(y=module), inherit.aes=FALSE, data=cur_DMEs)

        plot_list[[cur_comp]] <- p

      }

  } else{

    # this is for the condition: missing(group.by) && missing(comparison)

    print('Please be aware comparison group/groups are not provided, which may casue an ERROR. PlotDMEslollipop function will automatically assume all values are within the same group.')

    plot_list <- list()

    cur_DMEs <- DMEs

    # set plotting attributes for shape

    p <- Plotlollipop(modules, cur_DMEs, pvalue, avg_log2FC = 'avg_log2FC')

    p <- p + NoLegend() +  ggforestplot::geom_stripes(aes(y=module), inherit.aes=FALSE, data=cur_DMEs)

    plot_list <- p

  }

  return(plot_list)

}

#' Plotlollipop

#'

#' An Internal function for PlotDMEslollipop to Plotting function for the results of FindDMEs and FindAllDMEs

#'

#' @param seurat_obj A Seurat object

#' @param DMEs dataframe output from FindDMEs or FindAllDMEs

#' @param group.by the column name of the selected comparison in the DMEs dataframe

#' @param comparison character vector or a list of character vectors containing the comparison in the DMEs dataframe

#' @param pvalue p_value or fdr used for the comparison in the DMEs dataframe

#' @keywords scRNA-seq

#' @return A ggplot object

#' @examples

#' plot_list <- Plotlollipop(modules, DMEs, cur_title= c("Group1_vs_Group2"), pvalue, avg_log2FC = 'avg_log2FC')

Plotlollipop <- function(

  modules,

  cur_DMEs,

  pvalue,

  avg_log2FC = 'avg_log2FC'

){

#

    # cur_DMEs <- DMEs

    # set plotting attributes for shape

    cur_DMEs$shape <- ifelse(cur_DMEs[[pvalue]] < 0.05, 21, 4) # 21 cicle; 4 X

    cur_DMEs <- cur_DMEs %>% arrange(avg_log2FC, descending=TRUE)

    cur_DMEs$module <- factor(as.character(cur_DMEs$module), levels=as.character(cur_DMEs$module))

    # add number of genes per module

    n_genes <- table(modules$module)

    cur_DMEs$n_genes <- as.numeric(n_genes[as.character(cur_DMEs$module)])

    mod_colors <- dplyr::select(modules, c(module, color)) %>% distinct

    cp <- mod_colors$color; names(cp) <- mod_colors$module

    p <- cur_DMEs %>%

    ggplot(aes(y=module, x=avg_log2FC, size=log(n_genes), color=module)) +

    geom_vline(xintercept=0, color='black') +

    geom_segment(aes(y=module, yend=module, x=0, xend=avg_log2FC), linewidth=0.5, alpha=0.3) +

    geom_point() +

    geom_point(shape=cur_DMEs$shape, color='black', fill=NA) +

    scale_color_manual(values=cp, guide='none') +

    ylab('') +

    xlab(bquote("Avg. log"[2]~"(Fold Change)")) +

    theme(

        axis.line.y = element_blank(),

        axis.ticks.y = element_blank(),

        plot.title = element_text(hjust=0.5, face='plain', size=10)

    )

    return(p)

}