R/compare.vectors.R
In publicus/r-veccompare: Perform Set Operations on Vectors, Automatically Generating All n-Wise Comparisons, and Create Markdown Output
#' Compare all combinations of vectors using set operations
#'
#' @inheritParams render.venn.diagram
#' @param named_list_of_vectors_to_compare A named list of vectors to compare (see, for example, \code{\link{example.vectors.list}}). Duplicate values in a given vector will only be counted once (for example, c("a", "a", "b", "c") will be treated identically to c("a", "b", "c").
#' @param degrees_of_comparison_to_include A number or vector of numbers of which degrees of comparison to print (for example, 'c(2, 5)' would print only 2- and 5-way vector comparisons).
#' @param draw_venn_diagrams A logical (TRUE/FALSE) indicator whether to draw Venn diagrams for all 2- through 5-way comparisons of vectors.
#' @param vector_colors_for_venn_diagrams An optional vector of color names for Venn diagrams (if \code{draw_venn_diagrams} is \code{TRUE}). Color names are applied to the named vectors in \code{named_list_of_vectors_to_compare} in their order in \code{named_list_of_vectors_to_compare}. If this is blank, a random color will be selected for each vector. Either way, each vector will have a consistent color across the Venn diagrams in which it appears.
#' @param save_venn_diagram_files A logical (TRUE/FALSE) indicator whether to save Venn diagrams as PNG files.
#' @param location_for_venn_diagram_files An optional string giving a directory into which to save Venn diagram PNG files (if \code{save_venn_diagram_files} is \code{TRUE}). This location must already exist on the filesystem.
#' @param prefix_for_venn_diagram_files An optional string giving a prefix to prepend to saved Venn diagram PNG files (if \code{save_venn_diagram_files} is \code{TRUE}).
#' @param saved_venn_diagram_resolution_ppi An optional number giving a resolution (PPI) for saved Venn diagrams (if \code{save_venn_diagram_files} is \code{TRUE}).
#' @param saved_venn_diagram_dimension_units An optional string giving units for specifying \code{saved_venn_diagram_width} and \code{saved_venn_diagram_height} (if \code{save_venn_diagram_files} is \code{TRUE}). Can be \code{px} (pixels), \code{in} (inches, the default), \code{cm}, or \code{mm}.
#' @param saved_venn_diagram_width The width (in \code{saved_venn_diagram_dimension_units} units) for saved Venn diagrams (if \code{save_venn_diagram_files} is \code{TRUE}).
#' @param saved_venn_diagram_height The height (in \code{saved_venn_diagram_dimension_units} units) for saved Venn diagrams (if \code{save_venn_diagram_files} is \code{TRUE}).
#'
#' @param suppress_messages A logical (TRUE/FALSE) indicator whether to suppress messages. Even if this is \code{TRUE}, warnings will still be printed.
#'
#' @return A list, with one object for each comparison of vectors. The list contains the following elements:
#' \describe{
#' \item{elements_involved}{The vector names involved in the comparison.}
#' \item{union_of_elements}{A vector of all (deduplicated) items involved in the comparison, across all of the vectors.}
#' \item{overlap_of_elements}{A vector of the deduplicated elements that occurred in all of the compared vectors.}
#' \item{elements_unique_to_first_element}{This element will have a sub-element named for each vector being compared (i.e., for each of the names in \code{$elements_involved}). The (deduplicated) items that were unique to that vector (i.e., not overlapping with any other vector in the comparison).}
#' \item{venn_diagram}{If \code{save_venn_diagram_files} is \code{TRUE}, and the comparison is of 2 through 5 vectors, a Venn diagram object produced using the \pkg{VennDiagram} package. This diagram can be rendered using \code{\link{render.venn.diagram}}.}
#' }
#'
#' To compile this list object into a Markdown report, use \code{\link{compare.vectors.and.return.text.analysis.of.overlap}}. For an example of this usage, see the \code{Veccompare Overlap Report} RMarkdown template for RStudio that is installed as part of the \pkg{veccompare} package.
#' @export compare.vectors
#'
#' @examples
#' example <- veccompare::compare.vectors(veccompare::example.vectors.list)
#'
#' # To extract similar elements across list items:
#' veccompare::extract.compared.vectors(
#' example,
#' elements_of_output = "elements_involved"
#' )
#'
#' # To extract all comparisons that involve "vector_a":
#' veccompare::extract.compared.vectors(
#' example,
#' vector_names = "vector_a"
#' )
#'
#' # To find all comparisons that were about "vector_a" and "vector_c":
#' veccompare::extract.compared.vectors(
#' example,
#' vector_names = c("vector_a", "vector_c"),
#' only_match_vector_names = TRUE
#' )
#'
#' # To get all elements that did a two-way comparison:
#' veccompare::extract.compared.vectors(
#' example,
#' degrees_of_comparison = 2
#' )
compare.vectors <- function(
named_list_of_vectors_to_compare,
degrees_of_comparison_to_include = NULL,
draw_venn_diagrams = FALSE, # Whether we shold draw venn digrams for 2- to 5-way comparisons (the VennDiagram package can only draw up to five-way comparisons).
vector_colors_for_venn_diagrams = NULL,
save_venn_diagram_files = FALSE,
location_for_venn_diagram_files = "",
prefix_for_venn_diagram_files = "",
saved_venn_diagram_resolution_ppi = 300,
saved_venn_diagram_dimension_units = "in",
saved_venn_diagram_width = 8,
saved_venn_diagram_height = 6,
viewport_npc_width_height_for_images = 1.0,
suppress_messages = FALSE
){
vector_names <- names(named_list_of_vectors_to_compare)
degrees_of_comparison_to_include_after_figuring_venn_diagrams <- degrees_of_comparison_to_include # We'll update this as necessary as we go below.
degrees_of_comparison_for_venn_diagrams <- NULL # We'll also update this as necessary as we go below.
# If we're generating Venn diagrams, we'll create a consistent color to use for each vector:
if(draw_venn_diagrams == TRUE){
# Generate the combinations of vectors to use for Venn diagram drawing: ------------------------
# Figure out which degrees of comparison we need to calculate, especially if we're to draw Venn diagrams (which will require that, e.g., if we're drawing a 5-way comparison, we've also calculated all of the 1- to 4-way comparisons)
if(!is.null(degrees_of_comparison_to_include)){
maximum_degree_of_comparison_calculated <- max(degrees_of_comparison_to_include)
minimum_degree_of_comparison_calculated <- min(degrees_of_comparison_to_include)
if(draw_venn_diagrams == TRUE & maximum_degree_of_comparison_calculated >= 2 & minimum_degree_of_comparison_calculated <= 5){
degrees_of_comparison_for_venn_diagrams <- seq(
from = 2,
to = min(maximum_degree_of_comparison_calculated, 5) # We can only draw up to 5-way comparisons
)
degrees_of_comparison_to_include_after_figuring_venn_diagrams <- union(degrees_of_comparison_to_include, degrees_of_comparison_for_venn_diagrams)
degrees_of_comparison_to_include_after_figuring_venn_diagrams <- degrees_of_comparison_to_include_after_figuring_venn_diagrams[order(degrees_of_comparison_to_include_after_figuring_venn_diagrams)]
# Tell the user if there are elements that need to be computed in order to draw Venn diagrams but that weren't asked for:
degrees_of_comparison_not_asked_for_but_needed_for_diagrams <- degrees_of_comparison_for_venn_diagrams[which(! degrees_of_comparison_for_venn_diagrams %in% degrees_of_comparison_to_include)]
if(length(degrees_of_comparison_not_asked_for_but_needed_for_diagrams) > 0){
if(suppress_messages != TRUE){
message("Note: We need to calculate all combinations of degree(s) ", veccompare::vector.print.with.and(degrees_of_comparison_not_asked_for_but_needed_for_diagrams), " in addition to the degrees you asked for (", veccompare::vector.print.with.and(degrees_of_comparison_to_include), "), in order to draw Venn diagrams. Proceeding with calculating all of those...")
}
}
}
} else { # If degrees_of_comparison_to_include IS NULL:
maximum_degree_of_comparison_calculated <- length(named_list_of_vectors_to_compare)
if(draw_venn_diagrams == TRUE & maximum_degree_of_comparison_calculated >= 2){
degrees_of_comparison_for_venn_diagrams <- 2:(min(maximum_degree_of_comparison_calculated, 5)) # We can only draw up to 5-way comparisons
}
} # End of if(!is.null(degrees_of_comparison_to_include))
# Generate Venn diagram colors ------------------------
if(length(degrees_of_comparison_for_venn_diagrams) > 0){
if(!is.null(vector_colors_for_venn_diagrams)){
if(length(vector_colors_for_venn_diagrams) != length(vector_names)){
stop("The number of colors for Venn diagrams (", length(vector_colors_for_venn_diagrams), ") does not match the number of vectors we are comparing (", length(vector_names), ").")
} else {
vector_colors <- as.list(vector_colors_for_venn_diagrams)
names(vector_colors) <- vector_names
}
} else { # If we've not been given colors to use, we'll generate random ones:
vector_colors <- as.list(veccompare::generate.random.colors(length(vector_names)))
names(vector_colors) <- vector_names
}
} # End of if length(degrees_of_comparison_for_venn_diagrams) > 0
} # End of if draw_venn_diagrams == TRUE
combinations_of_vector_names <- as.data.frame(
gtools::combinations(
length(vector_names), # size of the source vector
length(vector_names), # size of the target vectors
vector_names,
set = TRUE, # Remove duplicates from the output
repeats.allowed = TRUE # Do all permutations of starting orders (vs. just combinations, where order doesn't matter). Setting this to TRUE will, when the items are chunked down, give us all 1:length(vector_names) sized combinations of items.
)
)
# Remove duplicate combinations, assessed after chunking down unique items in each row (so that, e.g., "a a a b" and "a a b b" are seen as the same thing, and only one of them is retained, since they both contain just elements "a" and "b"):
# The 'as.data.frame()' below is so that we know we're always dealing with a data.frame here -- if there's more than one combination of vector names, this would be a data.frame anyway, but if there's just one vector (and thus no combinations), this would otherwise be a factor. So setting this to be consistently a data.frame simplifies the steps below by allowing more consistency.
combinations_of_vector_names_chunked_for_unique_items <- as.data.frame(
combinations_of_vector_names[
!duplicated(
apply(
combinations_of_vector_names,
1, # iterate over rows
unique
)
)
, # Use all columns
]
)
# As a check of our work, this should usually be TRUE, unless length(vector_names) <= 2:
# nrow(combinations_of_vector_names_chunked_for_unique_items) < nrow(combinations_of_vector_names)
if(nrow(combinations_of_vector_names_chunked_for_unique_items) > 1){
rownames(combinations_of_vector_names_chunked_for_unique_items) <- NULL # This is just for aesthetic purposes; it makes debugging easier.
}
if(is.null(degrees_of_comparison_to_include)){ # If we *have not* been told which comparisons (e.g., 2-way, 3-way, etc.) to include, we'll use all of them by default:
combinations_of_vector_names_chunked_for_unique_items <- combinations_of_vector_names_chunked_for_unique_items
} else { # If we *have* been told which comparisons to include, we'll set that here:
if(!is.numeric(degrees_of_comparison_to_include)){
stop("The argument 'degrees_of_comparison_to_include' is expected to be numeric.")
} else { # If we are dealing with a numeric argument, as expected.
combinations_of_vector_names_chunked_for_unique_items <- combinations_of_vector_names_chunked_for_unique_items[
which(
apply(
combinations_of_vector_names_chunked_for_unique_items,
1, # Iterate over rows
function(x){length(unique(x)) %in% degrees_of_comparison_to_include_after_figuring_venn_diagrams}
)
)
, # Use all columns
]
if(suppress_messages != TRUE){
message("Calculating only the following degree(s) of comparison: ", veccompare::vector.print.with.and(degrees_of_comparison_to_include_after_figuring_venn_diagrams), "...")
}
}
}
combination_set_operations <- apply(
combinations_of_vector_names_chunked_for_unique_items,
1, # Iterate over rows
function(row){
# length(unique(x))
# print(row[1])
unique_names_in_row <- as.character(unique(row))
if(nrow(combinations_of_vector_names_chunked_for_unique_items) == 1){
vector_items_for_unique_names_in_row <- lapply(named_list_of_vectors_to_compare[unique_names_in_row], unique)
} else {
vector_items_for_unique_names_in_row <- named_list_of_vectors_to_compare[unique_names_in_row]
}
# Run setdiff() on with each element being first in turn (since setdiff gives the unique items for whichever item is printed first)
list_of_elements_unique_to_vectors = list() # We'll fill this in below.
for(vector_name in unique_names_in_row){
list_of_elements_unique_to_vectors[[vector_name]] = Reduce(
setdiff,
c(
vector_items_for_unique_names_in_row[vector_name], # Put vector_name first (since setdiff gives the unique items for whichever item is printed first)
vector_items_for_unique_names_in_row[-which( names(vector_items_for_unique_names_in_row) %in% vector_name)]
)
)
}
list_to_return <- list(
"elements_involved" = as.character(unique_names_in_row),
# The Reduce() approach below comes from https://www.r-bloggers.com/intersect-for-multiple-vectors-in-r/:
"union_of_elements" = Reduce(union, vector_items_for_unique_names_in_row),
"overlap_of_elements" = Reduce(intersect, vector_items_for_unique_names_in_row),
"elements_unique_to_first_element" = list_of_elements_unique_to_vectors
)
return(list_to_return)
}
)
# str(combination_set_operations)
# Draw Venn diagrams -------------------------------------------------
if(draw_venn_diagrams == TRUE){
# We will now create Venn diagrams for each level of comparison (e.g., 2-way, 3-way, etc.), from 2 to the maximum level of comparison (up to 5-way, since that's the most that the VennDiagram package I'm using can draw):
# Define a sub-function to make it easier to query overlaps between elements
get_overlap_of_elements_from_combination_set_operations <- function(
... # This should be a list of element names. "..." is R's way of accepting an arbitrary number of arguments.
){
element_names <- unlist(list(...)) # Parse the "..." arbitrary number of arguments into a vector.
overlap_value <- length(
combination_set_operations[[ # sapply() below should only bring back one matching element, since above we made sure we weren't calculating repeats, so this (just assuming that there will only be one matching element) seems safe to do.
which(
sapply(
purrr::map(combination_set_operations, "elements_involved"),
function(x){setequal(x, c(element_names))}
)
)
]]$overlap_of_elements
)
return(overlap_value)
} # End of sub-function definition
if(maximum_degree_of_comparison_calculated >= 2){
if(maximum_degree_of_comparison_calculated >= 6){
if(suppress_messages != TRUE){
message("Note: We can only draw up to 5-way diagrams. Thus, combinations of greater than 5 degrees (i.e., 6+ - way comparisons) will not be drawn...")
}
}
valid_venn_diagram_degrees_actually_asked_for_by_the_user <- degrees_of_comparison_for_venn_diagrams[degrees_of_comparison_for_venn_diagrams %in% degrees_of_comparison_to_include]
if(length(valid_venn_diagram_degrees_actually_asked_for_by_the_user) > 0){
if(suppress_messages != TRUE){
message("Drawing only the following degree(s) of comparison, following the options entered by the user: ", veccompare::vector.print.with.and(valid_venn_diagram_degrees_actually_asked_for_by_the_user), "...")
}
}
for(degree_of_comparison in valid_venn_diagram_degrees_actually_asked_for_by_the_user){ # The Venn Diagram package can only draw up to 5-way comparisons, so we won't go above 5 when drawing Venn-Diagrams.
if(suppress_messages != TRUE){
message("Calculating Venn diagram for all ", degree_of_comparison, "-way comparisons...", sep = "")
}
combination_set_elements_relevant_for_current_degree_of_comparison <- which(
sapply(
purrr::map(combination_set_operations, "elements_involved"),
function(x) {length(x) == degree_of_comparison}
)
)
for(combination_set_element_number in combination_set_elements_relevant_for_current_degree_of_comparison){
names_of_elements_in_this_comparison_set <- combination_set_operations[[combination_set_element_number]]$elements_involved
if(suppress_messages != TRUE){
message("Drawing comparison between ", veccompare::vector.print.with.and(names_of_elements_in_this_comparison_set), "...", sep = "")
}
if(length(names_of_elements_in_this_comparison_set) == 2){
venn_diagram <- VennDiagram::draw.pairwise.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
cross.area = length(combination_set_operations[[combination_set_element_number]]$overlap_of_elements),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 2), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 2),
cat.pos = rep(0, 2), # Category position around the circles (in degrees)
cat.dist = rep(0.025, 2), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 3),
cat.cex = rep(1.0, 2),
ind = FALSE # Do not automatically draw the diagram
)
} else if(length(names_of_elements_in_this_comparison_set) == 3){
venn_diagram <- VennDiagram::draw.triple.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
area3 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[3]]])),
n12 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2]),
n23 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n13 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3]),
n123 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 3), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 3),
cat.pos = c(315, 45, 180), # Category position around the circles (in degrees)
cat.dist = rep(0.025, 3), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 7),
cat.cex = rep(1.0, 3),
ind = FALSE # Do not automatically draw the diagram
)
} else if(length(names_of_elements_in_this_comparison_set) == 4){
venn_diagram <- VennDiagram::draw.quad.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
area3 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[3]]])),
area4 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[4]]])),
n12 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2]),
n13 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3]),
n14 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[4]),
n23 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n24 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n34 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n123 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n124 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n134 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n1234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 4), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 4),
#cat.pos = c(0, 0, 180), # Category position around the circles (in degrees)
#cat.dist = rep(0.025, 3), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 15),
cat.cex = rep(1.0, 4),
ind = FALSE # Do not automatically draw the diagram
)
} else if(length(names_of_elements_in_this_comparison_set) == 5){
venn_diagram <- VennDiagram::draw.quintuple.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
area3 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[3]]])),
area4 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[4]]])),
area5 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[5]]])),
n12 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2]),
n13 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3]),
n14 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[4]),
n15 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[5]),
n23 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n24 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n25 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[5]),
n34 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n35 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n45 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n123 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n124 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n125 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[5]),
n134 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n135 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n145 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n235 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n245 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n1234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n1235 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n1245 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n1345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n2345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n12345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 5), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 5),
#cat.pos = c(0, 0, 180), # Category position around the circles (in degrees)
#cat.dist = rep(0.025, 3), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 31),
cat.cex = rep(1.0, 5),
ind = FALSE # Do not automatically draw the diagram
)
} # End of if statement over length of elements
combination_set_operations[[combination_set_element_number]]$venn_diagram <- venn_diagram
if(save_venn_diagram_files == TRUE){
filename_to_use <- make.names(
paste(
paste(combination_set_operations[[combination_set_element_number]]$elements_involved, sep = "_vs_", collapse = "_vs_"),
"_venn_diagram.png",
sep = "",
collapse = ""
)
)
# Sanitize user inputs:
if(location_for_venn_diagram_files != ""){
location_for_venn_diagram_files_to_use <- as.character(location_for_venn_diagram_files)
} else {
location_for_venn_diagram_files_to_use <- getwd()
}
# Sanitize user inputs:
if(prefix_for_venn_diagram_files != ""){
prefix_for_venn_diagram_files_to_use <- as.character(prefix_for_venn_diagram_files)
} else {
prefix_for_venn_diagram_files_to_use <- ""
}
final_path_for_venn_diagram <- file.path(location_for_venn_diagram_files_to_use, paste(prefix_for_venn_diagram_files_to_use, filename_to_use, sep = ""))
if(suppress_messages != TRUE){
message("Saving Venn diagram to '", final_path_for_venn_diagram, "'...")
}
viewport_npc_width_height_for_images_value <- viewport_npc_width_height_for_images
# Begin pumping output into a PNG file:
png(
filename = final_path_for_venn_diagram,
res = saved_venn_diagram_resolution_ppi,
units = saved_venn_diagram_dimension_units,
width = saved_venn_diagram_width,
height = saved_venn_diagram_height
#, bg = "transparent" # Create a transparent background
)
veccompare::render.venn.diagram(venn_diagram, viewport_npc_width_height_for_images = viewport_npc_width_height_for_images_value)
# Stop sending output to a PNG
dev.off()
} # End of if(save_venn_diagram_files == TRUE)
} # End of for loop over combination_set_element_number
} # End of for loop over degree_of_comparison
} # End of if statement re: draw_venn_diagrams
} # End of if statement re: whether length(maximum_degree_of_comparison_calculated) > 1
# End of Draw Venn diagrams -------------------------------------------------
# To test the last-drawn diagram:
# grid::grid.newpage()
# grid::grid.draw(venn_diagram)
return(combination_set_operations)
} # End of function definition
publicus/r-veccompare documentation built on May 10, 2019, 1:18 p.m.
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#' Compare all combinations of vectors using set operations
#'
#' @inheritParams render.venn.diagram
#' @param named_list_of_vectors_to_compare A named list of vectors to compare (see, for example, \code{\link{example.vectors.list}}). Duplicate values in a given vector will only be counted once (for example, c("a", "a", "b", "c") will be treated identically to c("a", "b", "c").
#' @param degrees_of_comparison_to_include A number or vector of numbers of which degrees of comparison to print (for example, 'c(2, 5)' would print only 2- and 5-way vector comparisons).
#' @param draw_venn_diagrams A logical (TRUE/FALSE) indicator whether to draw Venn diagrams for all 2- through 5-way comparisons of vectors.
#' @param vector_colors_for_venn_diagrams An optional vector of color names for Venn diagrams (if \code{draw_venn_diagrams} is \code{TRUE}). Color names are applied to the named vectors in \code{named_list_of_vectors_to_compare} in their order in \code{named_list_of_vectors_to_compare}. If this is blank, a random color will be selected for each vector. Either way, each vector will have a consistent color across the Venn diagrams in which it appears.
#' @param save_venn_diagram_files A logical (TRUE/FALSE) indicator whether to save Venn diagrams as PNG files.
#' @param location_for_venn_diagram_files An optional string giving a directory into which to save Venn diagram PNG files (if \code{save_venn_diagram_files} is \code{TRUE}). This location must already exist on the filesystem.
#' @param prefix_for_venn_diagram_files An optional string giving a prefix to prepend to saved Venn diagram PNG files (if \code{save_venn_diagram_files} is \code{TRUE}).
#' @param saved_venn_diagram_resolution_ppi An optional number giving a resolution (PPI) for saved Venn diagrams (if \code{save_venn_diagram_files} is \code{TRUE}).
#' @param saved_venn_diagram_dimension_units An optional string giving units for specifying \code{saved_venn_diagram_width} and \code{saved_venn_diagram_height} (if \code{save_venn_diagram_files} is \code{TRUE}). Can be \code{px} (pixels), \code{in} (inches, the default), \code{cm}, or \code{mm}.
#' @param saved_venn_diagram_width The width (in \code{saved_venn_diagram_dimension_units} units) for saved Venn diagrams (if \code{save_venn_diagram_files} is \code{TRUE}).
#' @param saved_venn_diagram_height The height (in \code{saved_venn_diagram_dimension_units} units) for saved Venn diagrams (if \code{save_venn_diagram_files} is \code{TRUE}).
#'
#' @param suppress_messages A logical (TRUE/FALSE) indicator whether to suppress messages. Even if this is \code{TRUE}, warnings will still be printed.
#'
#' @return A list, with one object for each comparison of vectors. The list contains the following elements:
#' \describe{
#' \item{elements_involved}{The vector names involved in the comparison.}
#' \item{union_of_elements}{A vector of all (deduplicated) items involved in the comparison, across all of the vectors.}
#' \item{overlap_of_elements}{A vector of the deduplicated elements that occurred in all of the compared vectors.}
#' \item{elements_unique_to_first_element}{This element will have a sub-element named for each vector being compared (i.e., for each of the names in \code{$elements_involved}). The (deduplicated) items that were unique to that vector (i.e., not overlapping with any other vector in the comparison).}
#' \item{venn_diagram}{If \code{save_venn_diagram_files} is \code{TRUE}, and the comparison is of 2 through 5 vectors, a Venn diagram object produced using the \pkg{VennDiagram} package. This diagram can be rendered using \code{\link{render.venn.diagram}}.}
#' }
#'
#' To compile this list object into a Markdown report, use \code{\link{compare.vectors.and.return.text.analysis.of.overlap}}. For an example of this usage, see the \code{Veccompare Overlap Report} RMarkdown template for RStudio that is installed as part of the \pkg{veccompare} package.
#' @export compare.vectors
#'
#' @examples
#' example <- veccompare::compare.vectors(veccompare::example.vectors.list)
#'
#' # To extract similar elements across list items:
#' veccompare::extract.compared.vectors(
#' example,
#' elements_of_output = "elements_involved"
#' )
#'
#' # To extract all comparisons that involve "vector_a":
#' veccompare::extract.compared.vectors(
#' example,
#' vector_names = "vector_a"
#' )
#'
#' # To find all comparisons that were about "vector_a" and "vector_c":
#' veccompare::extract.compared.vectors(
#' example,
#' vector_names = c("vector_a", "vector_c"),
#' only_match_vector_names = TRUE
#' )
#'
#' # To get all elements that did a two-way comparison:
#' veccompare::extract.compared.vectors(
#' example,
#' degrees_of_comparison = 2
#' )
compare.vectors <- function(
named_list_of_vectors_to_compare,
degrees_of_comparison_to_include = NULL,
draw_venn_diagrams = FALSE, # Whether we shold draw venn digrams for 2- to 5-way comparisons (the VennDiagram package can only draw up to five-way comparisons).
vector_colors_for_venn_diagrams = NULL,
save_venn_diagram_files = FALSE,
location_for_venn_diagram_files = "",
prefix_for_venn_diagram_files = "",
saved_venn_diagram_resolution_ppi = 300,
saved_venn_diagram_dimension_units = "in",
saved_venn_diagram_width = 8,
saved_venn_diagram_height = 6,
viewport_npc_width_height_for_images = 1.0,
suppress_messages = FALSE
){
vector_names <- names(named_list_of_vectors_to_compare)
degrees_of_comparison_to_include_after_figuring_venn_diagrams <- degrees_of_comparison_to_include # We'll update this as necessary as we go below.
degrees_of_comparison_for_venn_diagrams <- NULL # We'll also update this as necessary as we go below.
# If we're generating Venn diagrams, we'll create a consistent color to use for each vector:
if(draw_venn_diagrams == TRUE){
# Generate the combinations of vectors to use for Venn diagram drawing: ------------------------
# Figure out which degrees of comparison we need to calculate, especially if we're to draw Venn diagrams (which will require that, e.g., if we're drawing a 5-way comparison, we've also calculated all of the 1- to 4-way comparisons)
if(!is.null(degrees_of_comparison_to_include)){
maximum_degree_of_comparison_calculated <- max(degrees_of_comparison_to_include)
minimum_degree_of_comparison_calculated <- min(degrees_of_comparison_to_include)
if(draw_venn_diagrams == TRUE & maximum_degree_of_comparison_calculated >= 2 & minimum_degree_of_comparison_calculated <= 5){
degrees_of_comparison_for_venn_diagrams <- seq(
from = 2,
to = min(maximum_degree_of_comparison_calculated, 5) # We can only draw up to 5-way comparisons
)
degrees_of_comparison_to_include_after_figuring_venn_diagrams <- union(degrees_of_comparison_to_include, degrees_of_comparison_for_venn_diagrams)
degrees_of_comparison_to_include_after_figuring_venn_diagrams <- degrees_of_comparison_to_include_after_figuring_venn_diagrams[order(degrees_of_comparison_to_include_after_figuring_venn_diagrams)]
# Tell the user if there are elements that need to be computed in order to draw Venn diagrams but that weren't asked for:
degrees_of_comparison_not_asked_for_but_needed_for_diagrams <- degrees_of_comparison_for_venn_diagrams[which(! degrees_of_comparison_for_venn_diagrams %in% degrees_of_comparison_to_include)]
if(length(degrees_of_comparison_not_asked_for_but_needed_for_diagrams) > 0){
if(suppress_messages != TRUE){
message("Note: We need to calculate all combinations of degree(s) ", veccompare::vector.print.with.and(degrees_of_comparison_not_asked_for_but_needed_for_diagrams), " in addition to the degrees you asked for (", veccompare::vector.print.with.and(degrees_of_comparison_to_include), "), in order to draw Venn diagrams. Proceeding with calculating all of those...")
}
}
}
} else { # If degrees_of_comparison_to_include IS NULL:
maximum_degree_of_comparison_calculated <- length(named_list_of_vectors_to_compare)
if(draw_venn_diagrams == TRUE & maximum_degree_of_comparison_calculated >= 2){
degrees_of_comparison_for_venn_diagrams <- 2:(min(maximum_degree_of_comparison_calculated, 5)) # We can only draw up to 5-way comparisons
}
} # End of if(!is.null(degrees_of_comparison_to_include))
# Generate Venn diagram colors ------------------------
if(length(degrees_of_comparison_for_venn_diagrams) > 0){
if(!is.null(vector_colors_for_venn_diagrams)){
if(length(vector_colors_for_venn_diagrams) != length(vector_names)){
stop("The number of colors for Venn diagrams (", length(vector_colors_for_venn_diagrams), ") does not match the number of vectors we are comparing (", length(vector_names), ").")
} else {
vector_colors <- as.list(vector_colors_for_venn_diagrams)
names(vector_colors) <- vector_names
}
} else { # If we've not been given colors to use, we'll generate random ones:
vector_colors <- as.list(veccompare::generate.random.colors(length(vector_names)))
names(vector_colors) <- vector_names
}
} # End of if length(degrees_of_comparison_for_venn_diagrams) > 0
} # End of if draw_venn_diagrams == TRUE
combinations_of_vector_names <- as.data.frame(
gtools::combinations(
length(vector_names), # size of the source vector
length(vector_names), # size of the target vectors
vector_names,
set = TRUE, # Remove duplicates from the output
repeats.allowed = TRUE # Do all permutations of starting orders (vs. just combinations, where order doesn't matter). Setting this to TRUE will, when the items are chunked down, give us all 1:length(vector_names) sized combinations of items.
)
)
# Remove duplicate combinations, assessed after chunking down unique items in each row (so that, e.g., "a a a b" and "a a b b" are seen as the same thing, and only one of them is retained, since they both contain just elements "a" and "b"):
# The 'as.data.frame()' below is so that we know we're always dealing with a data.frame here -- if there's more than one combination of vector names, this would be a data.frame anyway, but if there's just one vector (and thus no combinations), this would otherwise be a factor. So setting this to be consistently a data.frame simplifies the steps below by allowing more consistency.
combinations_of_vector_names_chunked_for_unique_items <- as.data.frame(
combinations_of_vector_names[
!duplicated(
apply(
combinations_of_vector_names,
1, # iterate over rows
unique
)
)
, # Use all columns
]
)
# As a check of our work, this should usually be TRUE, unless length(vector_names) <= 2:
# nrow(combinations_of_vector_names_chunked_for_unique_items) < nrow(combinations_of_vector_names)
if(nrow(combinations_of_vector_names_chunked_for_unique_items) > 1){
rownames(combinations_of_vector_names_chunked_for_unique_items) <- NULL # This is just for aesthetic purposes; it makes debugging easier.
}
if(is.null(degrees_of_comparison_to_include)){ # If we *have not* been told which comparisons (e.g., 2-way, 3-way, etc.) to include, we'll use all of them by default:
combinations_of_vector_names_chunked_for_unique_items <- combinations_of_vector_names_chunked_for_unique_items
} else { # If we *have* been told which comparisons to include, we'll set that here:
if(!is.numeric(degrees_of_comparison_to_include)){
stop("The argument 'degrees_of_comparison_to_include' is expected to be numeric.")
} else { # If we are dealing with a numeric argument, as expected.
combinations_of_vector_names_chunked_for_unique_items <- combinations_of_vector_names_chunked_for_unique_items[
which(
apply(
combinations_of_vector_names_chunked_for_unique_items,
1, # Iterate over rows
function(x){length(unique(x)) %in% degrees_of_comparison_to_include_after_figuring_venn_diagrams}
)
)
, # Use all columns
]
if(suppress_messages != TRUE){
message("Calculating only the following degree(s) of comparison: ", veccompare::vector.print.with.and(degrees_of_comparison_to_include_after_figuring_venn_diagrams), "...")
}
}
}
combination_set_operations <- apply(
combinations_of_vector_names_chunked_for_unique_items,
1, # Iterate over rows
function(row){
# length(unique(x))
# print(row[1])
unique_names_in_row <- as.character(unique(row))
if(nrow(combinations_of_vector_names_chunked_for_unique_items) == 1){
vector_items_for_unique_names_in_row <- lapply(named_list_of_vectors_to_compare[unique_names_in_row], unique)
} else {
vector_items_for_unique_names_in_row <- named_list_of_vectors_to_compare[unique_names_in_row]
}
# Run setdiff() on with each element being first in turn (since setdiff gives the unique items for whichever item is printed first)
list_of_elements_unique_to_vectors = list() # We'll fill this in below.
for(vector_name in unique_names_in_row){
list_of_elements_unique_to_vectors[[vector_name]] = Reduce(
setdiff,
c(
vector_items_for_unique_names_in_row[vector_name], # Put vector_name first (since setdiff gives the unique items for whichever item is printed first)
vector_items_for_unique_names_in_row[-which( names(vector_items_for_unique_names_in_row) %in% vector_name)]
)
)
}
list_to_return <- list(
"elements_involved" = as.character(unique_names_in_row),
# The Reduce() approach below comes from https://www.r-bloggers.com/intersect-for-multiple-vectors-in-r/:
"union_of_elements" = Reduce(union, vector_items_for_unique_names_in_row),
"overlap_of_elements" = Reduce(intersect, vector_items_for_unique_names_in_row),
"elements_unique_to_first_element" = list_of_elements_unique_to_vectors
)
return(list_to_return)
}
)
# str(combination_set_operations)
# Draw Venn diagrams -------------------------------------------------
if(draw_venn_diagrams == TRUE){
# We will now create Venn diagrams for each level of comparison (e.g., 2-way, 3-way, etc.), from 2 to the maximum level of comparison (up to 5-way, since that's the most that the VennDiagram package I'm using can draw):
# Define a sub-function to make it easier to query overlaps between elements
get_overlap_of_elements_from_combination_set_operations <- function(
... # This should be a list of element names. "..." is R's way of accepting an arbitrary number of arguments.
){
element_names <- unlist(list(...)) # Parse the "..." arbitrary number of arguments into a vector.
overlap_value <- length(
combination_set_operations[[ # sapply() below should only bring back one matching element, since above we made sure we weren't calculating repeats, so this (just assuming that there will only be one matching element) seems safe to do.
which(
sapply(
purrr::map(combination_set_operations, "elements_involved"),
function(x){setequal(x, c(element_names))}
)
)
]]$overlap_of_elements
)
return(overlap_value)
} # End of sub-function definition
if(maximum_degree_of_comparison_calculated >= 2){
if(maximum_degree_of_comparison_calculated >= 6){
if(suppress_messages != TRUE){
message("Note: We can only draw up to 5-way diagrams. Thus, combinations of greater than 5 degrees (i.e., 6+ - way comparisons) will not be drawn...")
}
}
valid_venn_diagram_degrees_actually_asked_for_by_the_user <- degrees_of_comparison_for_venn_diagrams[degrees_of_comparison_for_venn_diagrams %in% degrees_of_comparison_to_include]
if(length(valid_venn_diagram_degrees_actually_asked_for_by_the_user) > 0){
if(suppress_messages != TRUE){
message("Drawing only the following degree(s) of comparison, following the options entered by the user: ", veccompare::vector.print.with.and(valid_venn_diagram_degrees_actually_asked_for_by_the_user), "...")
}
}
for(degree_of_comparison in valid_venn_diagram_degrees_actually_asked_for_by_the_user){ # The Venn Diagram package can only draw up to 5-way comparisons, so we won't go above 5 when drawing Venn-Diagrams.
if(suppress_messages != TRUE){
message("Calculating Venn diagram for all ", degree_of_comparison, "-way comparisons...", sep = "")
}
combination_set_elements_relevant_for_current_degree_of_comparison <- which(
sapply(
purrr::map(combination_set_operations, "elements_involved"),
function(x) {length(x) == degree_of_comparison}
)
)
for(combination_set_element_number in combination_set_elements_relevant_for_current_degree_of_comparison){
names_of_elements_in_this_comparison_set <- combination_set_operations[[combination_set_element_number]]$elements_involved
if(suppress_messages != TRUE){
message("Drawing comparison between ", veccompare::vector.print.with.and(names_of_elements_in_this_comparison_set), "...", sep = "")
}
if(length(names_of_elements_in_this_comparison_set) == 2){
venn_diagram <- VennDiagram::draw.pairwise.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
cross.area = length(combination_set_operations[[combination_set_element_number]]$overlap_of_elements),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 2), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 2),
cat.pos = rep(0, 2), # Category position around the circles (in degrees)
cat.dist = rep(0.025, 2), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 3),
cat.cex = rep(1.0, 2),
ind = FALSE # Do not automatically draw the diagram
)
} else if(length(names_of_elements_in_this_comparison_set) == 3){
venn_diagram <- VennDiagram::draw.triple.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
area3 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[3]]])),
n12 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2]),
n23 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n13 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3]),
n123 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 3), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 3),
cat.pos = c(315, 45, 180), # Category position around the circles (in degrees)
cat.dist = rep(0.025, 3), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 7),
cat.cex = rep(1.0, 3),
ind = FALSE # Do not automatically draw the diagram
)
} else if(length(names_of_elements_in_this_comparison_set) == 4){
venn_diagram <- VennDiagram::draw.quad.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
area3 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[3]]])),
area4 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[4]]])),
n12 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2]),
n13 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3]),
n14 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[4]),
n23 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n24 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n34 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n123 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n124 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n134 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n1234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 4), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 4),
#cat.pos = c(0, 0, 180), # Category position around the circles (in degrees)
#cat.dist = rep(0.025, 3), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 15),
cat.cex = rep(1.0, 4),
ind = FALSE # Do not automatically draw the diagram
)
} else if(length(names_of_elements_in_this_comparison_set) == 5){
venn_diagram <- VennDiagram::draw.quintuple.venn(
area1 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[1]]])),
area2 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[2]]])),
area3 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[3]]])),
area4 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[4]]])),
area5 = length(unique(named_list_of_vectors_to_compare[[names_of_elements_in_this_comparison_set[5]]])),
n12 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2]),
n13 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3]),
n14 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[4]),
n15 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[5]),
n23 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n24 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n25 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[5]),
n34 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n35 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n45 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n123 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3]),
n124 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4]),
n125 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[5]),
n134 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n135 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n145 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n235 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n245 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n1234 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4]),
n1235 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[5]),
n1245 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n1345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n2345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
n12345 = get_overlap_of_elements_from_combination_set_operations(names_of_elements_in_this_comparison_set[1], names_of_elements_in_this_comparison_set[2], names_of_elements_in_this_comparison_set[3], names_of_elements_in_this_comparison_set[4], names_of_elements_in_this_comparison_set[5]),
category = names_of_elements_in_this_comparison_set,
lty = rep("blank", 5), # Line dash pattern of the circles
fill = unlist(vector_colors[names_of_elements_in_this_comparison_set]),
alpha = rep(0.5, 5),
#cat.pos = c(0, 0, 180), # Category position around the circles (in degrees)
#cat.dist = rep(0.025, 3), # Category names' distances from the edges of the circles (can be negative)
scaled = TRUE,
margin = 0,
cex = rep(1.0, 31),
cat.cex = rep(1.0, 5),
ind = FALSE # Do not automatically draw the diagram
)
} # End of if statement over length of elements
combination_set_operations[[combination_set_element_number]]$venn_diagram <- venn_diagram
if(save_venn_diagram_files == TRUE){
filename_to_use <- make.names(
paste(
paste(combination_set_operations[[combination_set_element_number]]$elements_involved, sep = "_vs_", collapse = "_vs_"),
"_venn_diagram.png",
sep = "",
collapse = ""
)
)
# Sanitize user inputs:
if(location_for_venn_diagram_files != ""){
location_for_venn_diagram_files_to_use <- as.character(location_for_venn_diagram_files)
} else {
location_for_venn_diagram_files_to_use <- getwd()
}
# Sanitize user inputs:
if(prefix_for_venn_diagram_files != ""){
prefix_for_venn_diagram_files_to_use <- as.character(prefix_for_venn_diagram_files)
} else {
prefix_for_venn_diagram_files_to_use <- ""
}
final_path_for_venn_diagram <- file.path(location_for_venn_diagram_files_to_use, paste(prefix_for_venn_diagram_files_to_use, filename_to_use, sep = ""))
if(suppress_messages != TRUE){
message("Saving Venn diagram to '", final_path_for_venn_diagram, "'...")
}
viewport_npc_width_height_for_images_value <- viewport_npc_width_height_for_images
# Begin pumping output into a PNG file:
png(
filename = final_path_for_venn_diagram,
res = saved_venn_diagram_resolution_ppi,
units = saved_venn_diagram_dimension_units,
width = saved_venn_diagram_width,
height = saved_venn_diagram_height
#, bg = "transparent" # Create a transparent background
)
veccompare::render.venn.diagram(venn_diagram, viewport_npc_width_height_for_images = viewport_npc_width_height_for_images_value)
# Stop sending output to a PNG
dev.off()
} # End of if(save_venn_diagram_files == TRUE)
} # End of for loop over combination_set_element_number
} # End of for loop over degree_of_comparison
} # End of if statement re: draw_venn_diagrams
} # End of if statement re: whether length(maximum_degree_of_comparison_calculated) > 1
# End of Draw Venn diagrams -------------------------------------------------
# To test the last-drawn diagram:
# grid::grid.newpage()
# grid::grid.draw(venn_diagram)
return(combination_set_operations)
} # End of function definition
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