Add xticks, xlim, and ylim arguments to g_lineplot (#1244)

# Pull Request

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Fixes #1243

NEWS.md

@@ -4,6 +4,7 @@
 * Added `facet_var` to `g_lineplot` to allow plot faceting by a factor variable.
 * Updated `g_lineplot` legend to follow factor levels set by users.
 * Added examples and tests for `label_all` parameter to `extract_survival_biomarkers` and `extract_survival_subgroups`.
+* Added the `xticks`, `xlim`, and `ylim` arguments to `g_lineplot` to allow for customization of the x and y axes.
 
 ### Bug Fixes
 * Fixed bug in `s_ancova` that prevented statistics from being printed when arm levels include special characters.

R/argument_convention.R

@@ -67,6 +67,11 @@
 #' @param vars (`character`)\cr variable names for the primary analysis variable to be iterated over.
 #' @param var (`string`)\cr single variable name for the primary analysis variable.
 #' @param x (`numeric`)\cr vector of numbers we want to analyze.
+#' @param xlim (`numeric(2)`)\cr vector containing lower and upper limits for the x-axis, respectively.
+#'   If `NULL` (default), the default scale range is used.
+#' @param ylim (`numeric(2)`)\cr vector containing lower and upper limits for the y-axis, respectively.
+#'   If `NULL` (default), the default scale range is used.
+#'
 #'
 #' @details Although this function just returns `NULL` it has two uses, for
 #'   the `tern` users it provides a documentation of arguments that are

R/g_km.R

@@ -6,7 +6,7 @@
 #' including the number of patient at risk at given time and the median survival
 #' per group.
 #'
-#' @param df (`data.frame`)\cr data set containing all analysis variables.
+#' @inheritParams argument_convention
 #' @param variables (named `list`)\cr variable names. Details are:
 #'   * `tte` (`numeric`)\cr variable indicating time-to-event duration values.
 #'   * `is_event` (`logical`)\cr event variable. `TRUE` if event, `FALSE` if time to event is censored.
@@ -35,8 +35,6 @@
 #' @param yval (`string`)\cr type of plot, to be plotted on the y-axis. Options are `Survival` (default) and `Failure`
 #'   probability.
 #' @param ylab (`string`)\cr y-axis label.
-#' @param ylim (`numeric(2)`)\cr vector containing lower and upper limits for the y-axis, respectively.
-#'   If `NULL` (default), the minimum and maximum y-values displayed are used as limits.
 #' @param title (`string`)\cr plot title.
 #' @param footnotes (`string`)\cr plot footnotes.
 #' @param font_size (`numeric(1)`)\cr font size to use for all text.

R/g_lineplot.R

@@ -4,7 +4,7 @@
 #'
 #' Line plot with the optional table.
 #'
-#' @param df (`data.frame`)\cr data set containing all analysis variables.
+#' @inheritParams argument_convention
 #' @param alt_counts_df (`data.frame` or `NULL`)\cr data set that will be used (only)
 #'   to counts objects in groups for stratification.
 #' @param variables (named `character`) vector of variable names in `df` which should include:
@@ -46,6 +46,9 @@
 #' @param legend_position (`string`)\cr the position of the plot legend (`"none"`, `"left"`, `"right"`, `"bottom"`,
 #'   `"top"`, or a two-element numeric vector).
 #' @param ggtheme (`theme`)\cr a graphical theme as provided by `ggplot2` to control styling of the plot.
+#' @param xticks (`numeric` or `NULL`)\cr numeric vector of tick positions or a single number with spacing
+#'   between ticks on the x-axis, for use when `variables$x` is numeric. If `NULL` (default), [labeling::extended()] is
+#'   used to determine optimal tick positions on the x-axis. If `variables$x` is not numeric, this argument is ignored.
 #' @param x_lab (`string` or `NULL`)\cr x-axis label. If `NULL` then no label will be added.
 #' @param y_lab (`string` or `NULL`)\cr y-axis label. If `NULL` then no label will be added.
 #' @param y_lab_add_paramcd (`flag`)\cr whether `paramcd`, i.e. `unique(df[[variables["paramcd"]]])` should be added
@@ -140,6 +143,9 @@ g_lineplot <- function(df,
                        legend_title = NULL,
                        legend_position = "bottom",
                        ggtheme = nestcolor::theme_nest(),
+                       xticks = NULL,
+                       xlim = NULL,
+                       ylim = NULL,
                        x_lab = obj_label(df[[variables[["x"]]]]),
                        y_lab = NULL,
                        y_lab_add_paramcd = TRUE,
@@ -158,7 +164,9 @@ g_lineplot <- function(df,
   checkmate::assert_character(mid, null.ok = TRUE)
   checkmate::assert_character(interval, null.ok = TRUE)
   checkmate::assert_character(col, null.ok = TRUE)
-
+  checkmate::assert_numeric(xticks, null.ok = TRUE)
+  checkmate::assert_numeric(xlim, finite = TRUE, any.missing = FALSE, len = 2, sorted = TRUE, null.ok = TRUE)
+  checkmate::assert_numeric(ylim, finite = TRUE, any.missing = FALSE, len = 2, sorted = TRUE, null.ok = TRUE)
   checkmate::assert_string(title, null.ok = TRUE)
   checkmate::assert_string(subtitle, null.ok = TRUE)
 
@@ -353,8 +361,13 @@ g_lineplot <- function(df,
     }
   }
 
+  if (is.numeric(df_stats[[x]])) {
+    if (length(xticks) == 1) xticks <- seq(from = min(df_stats[[x]]), to = max(df_stats[[x]]), by = xticks)
+    p <- p + ggplot2::scale_x_continuous(breaks = if (!is.null(xticks)) xticks else waiver(), limits = xlim)
+  }
+
   p <- p +
-    ggplot2::scale_y_continuous(labels = scales::comma) +
+    ggplot2::scale_y_continuous(labels = scales::comma, limits = ylim) +
     ggplot2::labs(
       title = title,
       subtitle = subtitle,