Merge pull request #57 from filipamc19/add-new-functions

Added functions plot_distibution_partialTAI and plot_distribution_expression

R/plot_distribution_expression.R

@@ -0,0 +1,69 @@
+#' @title Comparing expression levels distributions across the different developmental stages
+#' @description \emph{plot_distribution_partialTAI} generates 2 plots that help to compare the distribution
+#' of expression levels through various developmental stages, highlighting each stage with 
+#' distinct colors.
+#' @param ExpressionSet a standard PhyloExpressionSet or DivergenceExpressionSet object.
+#' @param stages a numeric vector specifying the indices of the stages to compare. Each index 
+#' corresponds to a stage in the ExpressionSet. Starts in one.
+#' @param xlab label of x-axis.
+#' @param ylab label of y-axis.
+#' @param main figure title.
+#' @param seed defines the colors for the different developmetal stages
+#' @section Recomendation - Apply a square root transformation to enhance the visualization of differences 
+#' in the distributions: plot_distribution_partialTAI(tf(ExpressionSet, sqrt))
+#' @author Filipa Martins Costa
+#' @export
+
+plot_distribution_expression <- function(ExpressionSet,
+                                         stages = 1:(ncol(ExpressionSet)-2),
+                                         xlab = "Expression",
+                                         ylab = "Density",
+                                         main = "Density Distribution of Expression by Developmental Stage",
+                                         seed = 123){
+
+  is.ExpressionSet(ExpressionSet)
+
+  if (any(stages > ncol(ExpressionSet))) {
+    stop("Some indices in 'stages' exceed the number of columns in 'ExpressionSet'.")
+  }
+
+  expression_long <- tidyr::pivot_longer(
+    ExpressionSet[,c(2,stages+2)],
+    cols = -GeneID,
+    names_to = "Stage",
+    values_to = "Expression"
+  )
+
+  qual_col_pals <-  RColorBrewer::brewer.pal.info[ RColorBrewer::brewer.pal.info$category == 'qual',]
+  col_vector <- unlist(mapply( RColorBrewer::brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
+  set.seed(seed)
+  colors <- sample(col_vector, ncol(ExpressionSet)-1)
+
+  P1 <- ggplot2::ggplot(expression_long, ggplot2::aes(x = Expression, fill = Stage)) +
+    ggplot2::geom_density(alpha = 0.7, color = "black") +
+    ggplot2::labs(
+      x = xlab,
+      y = ylab
+    ) +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      plot.title = ggplot2::element_text(hjust = 0.5, size = 14),
+      axis.title = ggplot2::element_text(size = 12)
+    ) +
+    ggplot2::scale_fill_manual(values = colors)
+
+  P2 <- ggplot2::ggplot(expression_long, ggplot2::aes(x = Expression, y = Stage, fill = Stage)) +
+    ggridges::geom_density_ridges(alpha = 0.7, color = "black", scale = 1) + 
+    ggplot2::labs(
+      x = xlab,
+      y = ylab
+    ) +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      plot.title = ggplot2::element_text(hjust = 0.5, size = 14),
+      axis.title = ggplot2::element_text(size = 12)
+    ) +
+    ggplot2::scale_fill_manual(values = colors)
+
+  cowplot::plot_grid(P1, P2, labels = main)
+}

R/plot_distribution_partialTAI.R

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+#' @title Comparing partial TAI distributions across the different developmental stages
+#' @description \emph{plot_distribution_partialTAI} generates 2 plots that help to compare the distribution
+#' of partial TAI through various developmental stages, highlighting each stage with 
+#' distinct colors.
+#' @param ExpressionSet a standard PhyloExpressionSet or DivergenceExpressionSet object.
+#' @param stages a numeric vector specifying the indices of the stages to compare. Each index 
+#' corresponds to a stage in the ExpressionSet. Starts in one.
+#' @param xlab label of x-axis.
+#' @param ylab label of y-axis.
+#' @param main figure title.
+#' @param seed defines the colors for the different developmetal stages
+#' @section Recomendation - Apply a square root transformation to enhance the visualization of differences 
+#' in the distributions: plot_distribution_partialTAI(tf(ExpressionSet, sqrt))
+#' @author Filipa Martins Costa
+#' @export
+
+plot_distribution_partialTAI <- function(ExpressionSet,
+                                         stages = 1:ncol(ExpressionSet)-2,
+                                         xlab = "Partial TAI",
+                                         ylab = "Density",
+                                         main = "Density Distribution of Partial TAI by Developmental Stage",
+                                         seed = 123){
+
+  if (any(stages > ncol(ExpressionSet))) {
+    stop("Some indices in 'stages' exceed the number of columns in 'ExpressionSet'.")
+  }
+
+  partial_TAI_matrix <- pMatrix(ExpressionSet[,c(1,2,stages+3)])
+
+  partial_TAI_df <- tibble::rownames_to_column(as.data.frame(partial_TAI_matrix), var = "GeneID")
+  partial_TAI_long <- tidyr::pivot_longer(
+    partial_TAI_df,
+    cols = -GeneID,
+    names_to = "Stage",
+    values_to = "PartialTAI"
+  )
+
+  qual_col_pals <-  RColorBrewer::brewer.pal.info[ RColorBrewer::brewer.pal.info$category == 'qual',]
+  col_vector <- unlist(mapply( RColorBrewer::brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
+  set.seed(seed)
+  colors <- sample(col_vector, ncol(partial_TAI_df))
+
+  partial_TAI_long$Stage <- factor(partial_TAI_long$Stage, levels = colnames(partial_TAI_matrix))
+
+  P1 <- ggplot2::ggplot(partial_TAI_long, ggplot2::aes(x = PartialTAI, fill = Stage)) +
+    ggplot2::geom_density(alpha = 0.7, color = "black") +
+    ggplot2::labs(
+      x = xlab,
+      y = ylab
+    ) +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      plot.title = ggplot2::element_text(hjust = 0.5, size = 14),
+      axis.title = ggplot2::element_text(size = 12)
+    ) +
+    ggplot2::scale_fill_manual(values = colors)
+
+  P2 <- ggplot2::ggplot(partial_TAI_long, ggplot2::aes(x = PartialTAI, y = Stage, fill = Stage)) +
+    ggridges::geom_density_ridges(alpha = 0.7, color = "black", scale = 1) + 
+    ggplot2::labs(
+      x = xlab,
+      y = ylab
+    ) +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      plot.title = ggplot2::element_text(hjust = 0.5, size = 14),
+      axis.title =ggplot2:: element_text(size = 12)
+    ) +
+    ggplot2::scale_fill_manual(values = colors)
+
+  cowplot::plot_grid(P1, P2, labels = main)
+
+}