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Add option to stack children clones #16

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Add option to stack children clones #16

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5 changes: 3 additions & 2 deletions R/EvoFreq_funcs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
#'@param tm_frac Value between 0 and 1 that determines where the maximum growth rate is in the inferred origin sizes. Lower values result in earlier maximum growth
#'@param rescale_after_thresholding Boolean determining if frequencies should be rescaled after thresholding, so that frequencies are based on what was above the threshold.
#'@param shuffle_colors Boolean determining if colors should be shuffled before being assigned to each clone. Only applies when fill_value = NULL
#'@param stacked Boolean determining if subclones should be stacked or sister branches should be separated by their parent clone.
#'@return Formatted dataframe called a "freq_frame" containing the information needed to plot the frequency dynamics over time.
#'
#'@examples
Expand Down Expand Up @@ -93,7 +94,7 @@
#'default_cmap_evo_p <- plot_evofreq(freq_frame_default_color)
#'}
#'@export
get_evofreq <- function(size_df, clones, parents, fill_value=NULL, fill_range = NULL, time_pts=NULL, clone_cmap=NULL, threshold=0.01, scale_by_sizes_at_time = FALSE, data_type="size", interpolation_steps = 20, interp_method = "monoH.FC", fill_gaps_in_size = FALSE, test_links=TRUE, add_origin=FALSE, tm_frac=0.6, rescale_after_thresholding=FALSE, shuffle_colors=FALSE){
get_evofreq <- function(size_df, clones, parents, fill_value=NULL, fill_range = NULL, time_pts=NULL, clone_cmap=NULL, threshold=0.01, scale_by_sizes_at_time = FALSE, data_type="size", interpolation_steps = 20, interp_method = "monoH.FC", fill_gaps_in_size = FALSE, test_links=TRUE, add_origin=FALSE, tm_frac=0.6, rescale_after_thresholding=FALSE, shuffle_colors=FALSE, stacked=FALSE){
# # ## FOR TESTING ###
# data("example.easy.wide.with.attributes")
# ### Split dataframe into clone info and size info using fact timepoint column names can be converted to numeric values
Expand Down Expand Up @@ -170,7 +171,7 @@ get_evofreq <- function(size_df, clones, parents, fill_value=NULL, fill_range =
cat("\n")
print("Getting Plot Positions")
time_pts <- colnames(freq_mat)
plot_pos_df <- get_pos(clones, parents, freq_mat, as.numeric(time_pts))
plot_pos_df <- get_pos(clones, parents, freq_mat, as.numeric(time_pts), stacked)


if(interpolation_steps > 0){
Expand Down
13 changes: 10 additions & 3 deletions R/idx_funcs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ get_ancestor_idx_evo_freq <- function(clone_id, clone_list, parent_list){
return(ancestral_idx)
}

get_pos <- function(clones, parents, mut_mat, og_time_pts=NULL){
get_pos <- function(clones, parents, mut_mat, og_time_pts=NULL, stacked=FALSE){
### FOR TESTING ###
# parents <- parents
# clones <- clones
Expand Down Expand Up @@ -145,7 +145,11 @@ get_pos <- function(clones, parents, mut_mat, og_time_pts=NULL){
}
# n_children <- length(children_idx)### NOTE WAS HERE
# n_children <- length(children_idx)
spacing <- (parent_area - total_child_area)/(n_children+1)
if(stacked){
spacing <- (parent_area - total_child_area)/2
} else {
spacing <- (parent_area - total_child_area)/(n_children+1)
}
# spacing[spacing < 0] <- min(spacing[spacing >= 0]) ###TODO DOES THIS WORK?

### Get bottom of parent's polygon
Expand Down Expand Up @@ -185,7 +189,10 @@ get_pos <- function(clones, parents, mut_mat, og_time_pts=NULL){
bottom <- loc
loc <- loc + child_size
top <- loc
loc <- loc + spacing

if(!stacked){
loc <- loc + spacing
}

# if(any(is.na(bottom))){
# print(paste("bottom positions are NA for clone", clone_id))
Expand Down