Addition of mStat_get_palette Function and Update of Palette Paramete…

…rs in Other Functions This update introduces significant enhancements in the color palette management across our visualization functionalities. ### Key Changes: 1. **Addition of `mStat_get_palette` Function**: A new function, `mStat_get_palette`, has been integrated into our codebase. This function provides a more versatile and robust approach to managing color palettes. It supports predefined palette names, custom color vectors, and ensures fallback to a default palette if needed. This enhancement allows for greater flexibility and ease of use in color customization for our users. 2. **Updates in Palette Parameter Usage**: We've updated several functions to utilize the new `mStat_get_palette` function. This change ensures consistency in color palette handling across different parts of the application. The functions with updated palette parameters now benefit from the enhanced capabilities of `mStat_get_palette`, including access to a broader range of color options and more intuitive palette selection. 3. **Improved User Experience and Customization**: These updates collectively aim to enhance the user experience by providing more control over color scheme selections in heatmap visualizations. Users can now easily select from a range of predefined color palettes or define their own, enhancing the visual appeal and interpretability of their heatmaps.
cafferychen777 · Jan 8, 2024 · dd3c0d4 · dd3c0d4
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diff --git a/NAMESPACE b/NAMESPACE
@@ -88,6 +88,7 @@ export(mStat_filter)
 export(mStat_generate_report_long)
 export(mStat_generate_report_pair)
 export(mStat_generate_report_single)
+export(mStat_get_palette)
 export(mStat_import_biom_as_data_obj)
 export(mStat_import_dada2_as_data_obj)
 export(mStat_import_mothur_as_data_obj)

diff --git a/R/generate_alpha_boxplot_long.R b/R/generate_alpha_boxplot_long.R
@@ -10,7 +10,15 @@
 #' @param time.var The variable in the metadata table that represents the time.
 #' @param t0.level Character or numeric, baseline time point for longitudinal analysis, e.g. "week_0" or 0. Required.
 #' @param ts.levels Character vector, names of follow-up time points, e.g. c("week_4", "week_8"). Required.
-#' @param palette An optional color palette for the plot. If not provided, a default color palette will be used. The palette should be a vector of color codes in a format accepted by ggplot2 (e.g., hexadecimal color codes). The number of colors in the palette should be at least as large as the number of groups being plotted.
+#' @param palette An optional parameter specifying the color palette to be used for the plot.
+#'                It can be either a character string specifying the name of a predefined
+#'                palette or a vector of color codes in a format accepted by ggplot2
+#'                (e.g., hexadecimal color codes). Available predefined palettes include
+#'                'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired
+#'                by various scientific publications and the `ggsci` package. If `palette`
+#'                is not provided or an unrecognized palette name is given, a default color
+#'                palette will be used. Ensure the number of colors in the palette is at
+#'                least as large as the number of groups being plotted.
 #' @param group.var An optional variable in the metadata table that represents the grouping factor.
 #' @param strata.var An optional variable in the metadata table that represents the stratification factor.
 #' @param adj.vars A character vector of variable names to be used for adjustment.
@@ -117,7 +125,7 @@
 #'   adj.vars = NULL,
 #'   base.size = 16,
 #'   theme.choice = "bw",
-#'   palette = NULL,
+#'   palette = "lancet",
 #'   pdf = TRUE,
 #'   file.ann = NULL,
 #'   pdf.wid = 20,
@@ -224,23 +232,8 @@ generate_alpha_boxplot_long <- function (data.obj,
       custom.theme else
     theme_function
 
-  if (is.null(palette)) {
-    col <-
-      c(
-        "#E31A1C",
-        "#1F78B4",
-        "#FB9A99",
-        "#33A02C",
-        "#FDBF6F",
-        "#B2DF8A",
-        "#A6CEE3",
-        "#BA7A70",
-        "#9D4E3F",
-        "#829BAB"
-      )
-  } else{
-    col <- palette
-  }
+  # Use mStat_get_palette to set the color palette
+  col <- mStat_get_palette(palette)
 
   if (is.null(group.var)) {
     alpha_df <- alpha_df %>% dplyr::mutate("ALL" = "ALL")

diff --git a/R/generate_alpha_boxplot_single.R b/R/generate_alpha_boxplot_single.R
@@ -30,7 +30,15 @@
 #' ```
 #'
 #' Then pass `my_theme` to `custom.theme`. Default is NULL, which will use the default theme based on `theme.choice`.
-#' @param palette An optional palette to use for the plot. If NULL (default), a pre-defined palette will be used.
+#' @param palette An optional parameter specifying the color palette to be used for the plot.
+#'                It can be either a character string specifying the name of a predefined
+#'                palette or a vector of color codes in a format accepted by ggplot2
+#'                (e.g., hexadecimal color codes). Available predefined palettes include
+#'                'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired
+#'                by various scientific publications and the `ggsci` package. If `palette`
+#'                is not provided or an unrecognized palette name is given, a default color
+#'                palette will be used. Ensure the number of colors in the palette is at
+#'                least as large as the number of groups being plotted.
 #' @param pdf A boolean indicating whether to save the output as a PDF file. Default is TRUE.
 #' @param file.ann A string for annotating the output file name.
 #' @param pdf.wid The width of the output PDF file. Default is 11.
@@ -130,7 +138,7 @@
 #'   adj.vars     = "sex",
 #'   base.size    = 16,
 #'   theme.choice = "bw",
-#'   palette      = NULL,
+#'   palette      = "lancet",
 #'   pdf          = FALSE,
 #'   file.ann     = NULL,
 #'   pdf.wid      = 11,
@@ -209,23 +217,7 @@ generate_alpha_boxplot_single <- function (data.obj,
   else
     theme_function
 
-  if (is.null(palette)) {
-    col <-
-      c(
-        "#E31A1C",
-        "#1F78B4",
-        "#FB9A99",
-        "#33A02C",
-        "#FDBF6F",
-        "#B2DF8A",
-        "#A6CEE3",
-        "#BA7A70",
-        "#9D4E3F",
-        "#829BAB"
-      )
-  } else{
-    col <- palette
-  }
+  col <- mStat_get_palette(palette)
 
   # Create a plot for each alpha diversity index
   plot_list <- lapply(alpha.name, function(index) {

diff --git a/R/generate_alpha_change_boxplot_pair.R b/R/generate_alpha_change_boxplot_pair.R
@@ -53,7 +53,15 @@
 #' ```
 #'
 #' Then pass `my_theme` to `custom.theme`. Default is NULL, which will use the default theme based on `theme.choice`.
-#' @param palette An optional color palette for the plot. If not provided, a default color palette will be used. The palette should be a vector of color codes in a format accepted by ggplot2 (e.g., hexadecimal color codes). The number of colors in the palette should be at least as large as the number of groups being plotted.
+#' @param palette An optional parameter specifying the color palette to be used for the plot.
+#'                It can be either a character string specifying the name of a predefined
+#'                palette or a vector of color codes in a format accepted by ggplot2
+#'                (e.g., hexadecimal color codes). Available predefined palettes include
+#'                'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired
+#'                by various scientific publications and the `ggsci` package. If `palette`
+#'                is not provided or an unrecognized palette name is given, a default color
+#'                palette will be used. Ensure the number of colors in the palette is at
+#'                least as large as the number of groups being plotted.
 #' @param pdf.wid The width of the output PDF file. Default is 11.
 #' @param pdf.hei The height of the output PDF file. Default is 8.5.
 #' @param subject.var The variable in the metadata table that represents the subject.
@@ -82,7 +90,7 @@
 #'   alpha.change.func = "absolute change",
 #'   base.size = 16,
 #'   theme.choice = "bw",
-#'   palette = NULL,
+#'   palette = "lancet",
 #'   pdf = TRUE,
 #'   file.ann = NULL,
 #'   pdf.wid = 11,
@@ -201,23 +209,7 @@ generate_alpha_change_boxplot_pair <-
 
     combined_alpha <- dplyr::bind_cols(combined_alpha, diff_columns)
 
-    if (is.null(palette)) {
-      col <-
-        c(
-          "#E31A1C",
-          "#1F78B4",
-          "#FB9A99",
-          "#33A02C",
-          "#FDBF6F",
-          "#B2DF8A",
-          "#A6CEE3",
-          "#BA7A70",
-          "#9D4E3F",
-          "#829BAB"
-        )
-    } else{
-      col <- palette
-    }
+    col <- mStat_get_palette(palette)
 
     facet_formula <-
       if (!is.null(strata.var)) {

diff --git a/R/generate_alpha_dotplot_long.R b/R/generate_alpha_dotplot_long.R
@@ -60,13 +60,13 @@
 #'   adj.vars = "sample_body_site"
 #' )
 #' # Visualizing the results for the Type 2 Diabetes dataset
-#' dotplot_T2D <- generate_taxa_dotplot_long(
+#' dotplot_T2D <- generate_alpha_dotplot_long(
 #'   data.obj = subset_T2D.obj,
 #'   test.list = result2,
 #'   group.var = "subject_race",
 #'   time.var = "visit_number",
 #'   t0.level = unique(subset_T2D.obj$meta.dat$visit_number)[1],
-#'   ts.levels = unique(subset_T2D.obj$meta.dat$visit_number)[-1],
+#'   ts.levels = unique(subset_T2D.obj$meta.dat$visit_number)[-1]
 #' )
 #' }
 #' @export
@@ -79,7 +79,7 @@ generate_alpha_dotplot_long <- function(data.obj,
                                         base.size = 16,
                                         theme.choice = "bw",
                                         custom.theme = NULL,
-                                        palette = NULL,
+                                        palette = rev(c("white", "#92c5de", "#0571b0", "#f4a582", "#ca0020")),
                                         pdf = FALSE,
                                         pdf.wid = 7,
                                         pdf.hei = 5
@@ -129,6 +129,8 @@ generate_alpha_dotplot_long <- function(data.obj,
 
   p_val_var <- "P.Value"
 
+  col <- mStat_get_palette(palette)
+
   plot.list <- lapply(group.names, function(group.names){
 
     data_for_plot <- test.list[[group.names]]
@@ -140,7 +142,7 @@ generate_alpha_dotplot_long <- function(data.obj,
     dotplot <- ggplot(data_for_plot, aes(x = !!sym(time.var), y = Term, size = Estimate)) +
       geom_point(aes(color = !!sym(p_val_var)), alpha = 0.6, shape = 19) +
       geom_text(aes(label = Significance_Label), vjust = 0.8, show.legend = FALSE, color = "white") +
-      scale_color_gradientn(colors = rev(c("white", "#92c5de", "#0571b0", "#f4a582", "#ca0020"))) +
+      scale_color_gradientn(colors = col) +
       labs(title = group.names,
            x = time.var,
            y = "Term",

diff --git a/R/generate_alpha_spaghettiplot_long.R b/R/generate_alpha_spaghettiplot_long.R
@@ -10,7 +10,15 @@
 #' @param t0.level Character or numeric, baseline time point for longitudinal analysis, e.g. "week_0" or 0. Required.
 #' @param ts.levels Character vector, names of follow-up time points, e.g. c("week_4", "week_8"). Required.
 #' @param base.size The base font size for the plot.
-#' @param palette An optional color palette for the plot. If not provided, a default color palette will be used. The palette should be a vector of color codes in a format accepted by ggplot2 (e.g., hexadecimal color codes). The number of colors in the palette should be at least as large as the number of groups being plotted.
+#' @param palette An optional parameter specifying the color palette to be used for the plot.
+#'                It can be either a character string specifying the name of a predefined
+#'                palette or a vector of color codes in a format accepted by ggplot2
+#'                (e.g., hexadecimal color codes). Available predefined palettes include
+#'                'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired
+#'                by various scientific publications and the `ggsci` package. If `palette`
+#'                is not provided or an unrecognized palette name is given, a default color
+#'                palette will be used. Ensure the number of colors in the palette is at
+#'                least as large as the number of groups being plotted.
 #' @param theme.choice Plot theme choice. Can be one of:
 #'   - "prism": ggprism::theme_prism()
 #'   - "classic": theme_classic()
@@ -44,7 +52,6 @@
 #' \dontrun{
 #' data("subset_T2D.obj")
 #' T2D.alpha.obj <- mStat_calculate_alpha_diversity(subset_T2D.obj$feature.tab,"shannon")
-#'
 #' generate_alpha_spaghettiplot_long(
 #'   data.obj = subset_T2D.obj,
 #'   alpha.obj = T2D.alpha.obj,
@@ -57,7 +64,27 @@
 #'   strata.var = "subject_race",
 #'   adj.vars = "sample_body_site",
 #'   theme.choice = "bw",
-#'   palette = NULL,
+#'   palette = "lancet",
+#'   pdf = TRUE,
+#'   file.ann = NULL,
+#'   pdf.wid = 11,
+#'   pdf.hei = 8.5
+#' )
+#'
+#' data("ecam.obj")
+#' generate_alpha_spaghettiplot_long(
+#'   data.obj = ecam.obj,
+#'   alpha.obj = NULL,
+#'   alpha.name = c("shannon","simpson", "observed_species"),
+#'   subject.var = "subject.id",
+#'   time.var = "month_num",
+#'   t0.level = NULL,
+#'   ts.levels = NULL,
+#'   group.var = "delivery",
+#'   strata.var = "diet",
+#'   adj.vars = NULL,
+#'   theme.choice = "bw",
+#'   palette = "lancet",
 #'   pdf = TRUE,
 #'   file.ann = NULL,
 #'   pdf.wid = 11,
@@ -167,23 +194,7 @@ generate_alpha_spaghettiplot_long <-
 
     theme_to_use <- if (!is.null(custom.theme)) custom.theme else theme_function
 
-    if (is.null(palette)){
-      col <-
-        c(
-          "#E31A1C",
-          "#1F78B4",
-          "#FB9A99",
-          "#33A02C",
-          "#FDBF6F",
-          "#B2DF8A",
-          "#A6CEE3",
-          "#BA7A70",
-          "#9D4E3F",
-          "#829BAB"
-        )
-    } else{
-      col <- palette
-    }
+    col <- mStat_get_palette(palette)
 
     # Create a plot for each alpha diversity index
     plot_list <- lapply(alpha.name, function(index) {

diff --git a/R/generate_beta_change_boxplot_pair.R b/R/generate_beta_change_boxplot_pair.R
@@ -45,7 +45,15 @@
 #' ```
 #'
 #' Then pass `my_theme` to `custom.theme`. Default is NULL, which will use the default theme based on `theme.choice`.
-#' @param palette (Optional) A palette function or character vector with the colors for the plot.
+#' @param palette An optional parameter specifying the color palette to be used for the plot.
+#'                It can be either a character string specifying the name of a predefined
+#'                palette or a vector of color codes in a format accepted by ggplot2
+#'                (e.g., hexadecimal color codes). Available predefined palettes include
+#'                'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired
+#'                by various scientific publications and the `ggsci` package. If `palette`
+#'                is not provided or an unrecognized palette name is given, a default color
+#'                palette will be used. Ensure the number of colors in the palette is at
+#'                least as large as the number of groups being plotted.
 #' @param pdf A logical value indicating whether to save the plot as a PDF file. Default is TRUE
 #' @param file.ann A character string specifying a custom annotation for the PDF file name or NULL (default)
 #' @param pdf.wid (Optional) The width of the PDF file if `pdf` is set to `TRUE` (default is 11).
@@ -79,7 +87,7 @@
 #'   base.size = 20,
 #'   theme.choice = "bw",
 #'   custom.theme = NULL,
-#'   palette = NULL,
+#'   palette = "lancet",
 #'   pdf = TRUE,
 #'   file.ann = NULL,
 #'   pdf.wid = 11,
@@ -138,23 +146,7 @@ generate_beta_change_boxplot_pair <-
     change.after <-
       unique(meta_tab %>% dplyr::select(all_of(c(time.var))))[unique(meta_tab %>% dplyr::select(all_of(c(time.var)))) != change.base]
 
-    if (is.null(palette)){
-      col <-
-        c(
-          "#E31A1C",
-          "#1F78B4",
-          "#FB9A99",
-          "#33A02C",
-          "#FDBF6F",
-          "#B2DF8A",
-          "#A6CEE3",
-          "#BA7A70",
-          "#9D4E3F",
-          "#829BAB"
-        )
-    } else {
-      col <- palette
-    }
+    col <- mStat_get_palette(palette)
 
     theme_function <- switch(
       theme.choice,

diff --git a/R/generate_beta_change_spaghettiplot_long.R b/R/generate_beta_change_spaghettiplot_long.R
@@ -32,7 +32,15 @@
 #' ```
 #'
 #' Then pass `my_theme` to `custom.theme`. Default is NULL, which will use the default theme based on `theme.choice`.
-#' @param palette (Optional) A palette function or character vector with the colors for the plot.
+#' @param palette An optional parameter specifying the color palette to be used for the plot.
+#'                It can be either a character string specifying the name of a predefined
+#'                palette or a vector of color codes in a format accepted by ggplot2
+#'                (e.g., hexadecimal color codes). Available predefined palettes include
+#'                'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired
+#'                by various scientific publications and the `ggsci` package. If `palette`
+#'                is not provided or an unrecognized palette name is given, a default color
+#'                palette will be used. Ensure the number of colors in the palette is at
+#'                least as large as the number of groups being plotted.
 #' @param pdf (Optional) A boolean indicating whether to save the output as a PDF file (default is TRUE).
 #' @param file.ann (Optional) A string for annotating the output file name.
 #' @param pdf.wid (Optional) The width of the PDF file if `pdf` is set to `TRUE` (default is 11).
@@ -131,23 +139,7 @@ generate_beta_change_spaghettiplot_long <-
         !is.character(strata.var))
       stop("`strata.var` should be a character string or NULL.")
 
-    if (is.null(palette)){
-      col <-
-        c(
-          "#E31A1C",
-          "#1F78B4",
-          "#FB9A99",
-          "#33A02C",
-          "#FDBF6F",
-          "#B2DF8A",
-          "#A6CEE3",
-          "#BA7A70",
-          "#9D4E3F",
-          "#829BAB"
-        )
-    } else{
-      col <- palette
-    }
+    col <- mStat_get_palette(palette)
 
     theme_function <- switch(theme.choice,
                              prism = ggprism::theme_prism(),