Create a layout based on post probs, cyt heat map and scores

Usage

.save_layout(
  ind,
  p_list_pp,
  p_list_scores = NULL,
  prop_pp,
  shift_plot_heatmap_x,
  shift_plot_scores_y,
  shift_plot_pp_y,
  height,
  width,
  dir_save,
  file,
  save_format,
  label,
  n_col,
  shift_label,
  font_size_labels
)

Arguments

ind: logical. If TRUE, then sets of posterior probability and PFS plots are saved individually.
p_list_pp: list of ggplot2 objects. Posterior probability plots and associated cytokine-label grids, as returned by UtilsCompassSV:::.plot_compass_pp.
p_list_scores: list of ggplot2 objects. PFS and FS response plots, as returned by UtilsCompassSV:::.plot_compass_scores.
prop_pp: numeric vector, values in [0,1]. Specifies coordinate-wise the proportion of plot region for a single group in c_obj (if c_obj is a list; otherwise it's simply the proportion of the plot) that is devoted (before applying shift_plot_pp_y) to the plot of posterior probabilities. The first element is the proportion allocated to the probability plot along the x-axis, and (1-prop_pp[1]) is then the space allocated to the scores plot. The first element is set equal to 0 if there is no scores plot. The second element is the proportion allocate to the probabilty plot along the y-axis, and (1-prop_pp[1]) is then the space allocated to the cytokine indicator grid.
shift_plot_heatmap_x: [0,1]. Extent to shift prob_plot. Increasing it from 0 moves the start of the probability plot further to the right. Maximum value is 1 (at which point the plot will effectively be pushed off the plotting surface). Useful to increase to a value such as 0.01 if the cytokine names are long and push the labelling grid too far to the right. Tweak as required. Default is 0.
shift_plot_scores_y: numeric vector of length two, restricted to [-1,1]. Specifies the amount to squeeze the scores plot in. The first element controls the bottom position of the plot, and the second the top. For both elements, a positive value means moving upwards. A value of zero corresponds no shift. Typically the bottom element and top element should both be shifted down (and therefore have negative values). Only applies if type includes both "pp" and "scores". Default is c(0,0).
shift_plot_pp_y: [0,1]. Specifies amount by which to shift the upper point of the probability plot upwards. Positive values make it larger. Typically you want to shift this down, if anything, so use negative values. Default is 0.
height, width: numeric. Height and width of saved plot(s).
dir_save: character. Where to save the output. Default is working directory.
file: character. File name for the saved plot.
save_format: "pdf" or "png". Plot device to use. Default is "png".
label: logical. If TRUE and c_obj is a list, then the names of elements in c_obj are used as labels for sub-figures. If c_obj is not a list, then no label is printed, regardless of the value of label. Default is TRUE.
n_col: integer. Number of columns for the grid layout.
shift_label: numeric vector, values in [0,1]. Specifies amount by which to shift the labels of the plot (if used). Default is c(0.05, -0.04).
font_size_labels: numeric. Font size for plot labels.