main hm building function — plot_state

anno_cols_list: list(Passage=c(3: #123456))

Usage

plot_state_hm(
  states_df,
  state_col,
  phylogeny = NULL,
  anno_df = NULL,
  anno_colors_list = list(),
  clones_df = NULL,
  anno_columns = NULL,
  clone_column = NULL,
  color_tree_clones = FALSE,
  clone_palette = NULL,
  only_largest_clone_group = FALSE,
  file_name = NULL,
  labels_fontsize = 8,
  continuous_hm_colours = FALSE,
  custom_continuous_colors = NULL,
  custom_continuous_range = NULL,
  hm_discrete_colors = NULL,
  legend_11plus = FALSE,
  ...
)

Arguments

states_df: long format read bin data to be plotted
state_col: string of column name to target for plotting in the heatmap. Examples include: state, BAF, state_AS, state_phase
phylogeny: optional. phylo class object to be plotted.
anno_df: optional. annotations dataframe with cell_id column and annotation for each cell id to be added to a heatmap.
anno_colors_list: list of named vectors specifying colors for annotations example: list(passage=c(1='#2872bc', 19='#d23e3e'))
clones_df: optional. dataframe of clone ideas (clone_id) for each cell_id. Both columns required.
anno_columns: optional. Columns containing the annotation data to plot.
clone_column: optional. Column of clone id labels for cells.
color_tree_clones: boolean. optional. Whether to color the tree with the same colors as the clone labels.
clone_palette: optional. ideally a named vector on how to color clones. Vector names are clond ID, values are hex codes. If vector is unnamed, names will be assigned, but without control on which get's which color.
only_largest_clone_group: boolean. optional. Only put a letter label on the largest group of any given clone id.
file_name: name of the file to save the plot to. Recommended for most cases as plots are big-ish.
labels_fontsize: how large to make text labels
continuous_hm_colours: plot heatmap colors on a continous scale.
custom_continuous_colors: a vector of 3 colors to use as the scale for plotting a continuous variable, specified as hexcodes. E.g., c("#3182BD", "#CCCCCC", "#FDCC8A")
custom_continuous_range: a vector of values to specify as the low, mid, and high bounds for the continuous color scale, e.g., c(1, 5, 10)
hm_discrete_colors: specified colors for the values being plotted. Named vector: c(1="#3182BD", 2="#FDCC8A"). Need to specify for every value
legend_11plus: bool. Default FALSE. For HMMCopy state values, state 11 is really 11+, so we replace 11s with 11+ for the plot in the legend. being plotted