Plot a heat map of states across chromosomes. Put annotations next to it, a tree next to it, mark clone groups, or all of that at once!
Usage
plot_state_hm(
states_df,
state_col,
phylogeny = NULL,
file_name = NULL,
anno_df = NULL,
anno_colors_list = list(),
anno_columns = NULL,
clone_column = NULL,
clones_df = NULL,
clone_palette = NULL,
only_largest_clone_group = TRUE,
labels_fontsize = 8,
is_continuous = FALSE,
continuous_hm_colours = FALSE,
custom_continuous_colors = NULL,
custom_continuous_range = NULL,
hm_discrete_colors = NULL,
hm_legend_title = NULL,
legend_11plus = FALSE,
color_tree_clones = FALSE,
scale_y = FALSE,
cell_height = 10,
default_png_height = 1600,
annotation_legend_param = list(),
show_annotation_legend = TRUE,
annotation_name_gp = 16,
heatmap_legend_param = list(),
show_heatmap_legend = TRUE,
custom_legend = list(),
hm_title = NULL,
...
)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.
- file_name
name of the file to save the plot to. Recommended for most cases as plots are big-ish.
- 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(p1='#2872bc', p19='#d23e3e'))- anno_columns
optional. Columns containing the annotation data to plot.
- clone_column
optional. Column of clone id labels for cells.
- clones_df
optional. dataframe of clone ideas (clone_id) for each cell_id. Both columns required.
- 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.
- 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
- hm_legend_title
string. What to label the legend for what is plotted in the heatmap. Will default to the name of the column being plotted.
- 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.
- color_tree_clones
boolean. optional. Whether to color the tree with the same colors as the clone labels.
- scale_y
bool. Default FALSE. Scale the y size of the saved image accoring to the number of cells in the heatmap
- cell_height,
int. Default = 10 Heigh in pixels per cell if scale_y is True
- default_png_height,
int: Default = 1600. If scale_y not used, height of final png
- annotation_legend_param,
list(). Parameters topass to the annotation legend ex: annotation_legend_params <- list( Small_inter_few_telo = list( title_gp = grid::gpar(fontsize = 20), #fontsize of title labels_gp = grid::gpar(fontsize = 16), # fontsize of labels gp = grid::gpar(fontsize = 16) # siez of color bar or whatever legend is showing I think )
- show_annotation_legend,
bool.
- annotation_name_gp
Int: Fontsize for label names
- show_heatmap_legend,
bool
- custom_legend,
List(). custom legend for use when annotation and heatmap legends are FALSE For examples, see