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RDA: option for plotting centroids and species scores #155

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Oct 9, 2024
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RDA: option for plotting centroids and species scores #155

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TuomasBorman Oct 7, 2024
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TuomasBorman Oct 7, 2024
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TuomasBorman Oct 7, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: miaViz
Title: Microbiome Analysis Plotting and Visualization
Version: 1.13.13
Version: 1.13.14
Authors@R:
c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
email = "tuomas.v.borman@utu.fi",
Expand Down
113 changes: 78 additions & 35 deletions R/plotCCA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,12 @@
#'
#' \item \code{add.expl.var}: \code{Logical scalar}. Should explained
#' variance appear on the coordinate axes. (Default: \code{TRUE})
#'
#' \item \code{add.centroids}: \code{Logical scalar}. Should centroids
#' of variables be added. (Default: \code{FALSE})
#'
#' \item \code{add.species}: \code{Logical scalar}. Should species
#' scores be added. (Default: \code{FALSE})
#' }
#'
#'
Expand Down Expand Up @@ -229,6 +235,7 @@ setMethod("plotRDA", signature = c(x = "matrix"),
add.vectors = TRUE, vec.lab = NULL,
expl.var = expl_var, expl_var = NULL,
sep.group = "\U2014", repl.underscore = " ",
add.centroids = FALSE, add.species = FALSE,
# These parameters below are not used in this function. They are just
# catched so that they are not fed into scater::plotRecucedDim.
ellipse.alpha = 0.2, ellipse.linewidth = 0.1,
Expand Down Expand Up @@ -265,6 +272,12 @@ setMethod("plotRDA", signature = c(x = "matrix"),
if ( !.is_a_string(repl.underscore) ) {
stop("'repl.underscore' must be a string.", call. = FALSE)
}
if( !.is_a_bool(add.centroids) ){
stop("'add.centroids' must be TRUE or FALSE.", call. = FALSE)
}
if( !.is_a_bool(add.species) ){
stop("'add.species' must be TRUE or FALSE.", call. = FALSE)
}
###################### Input check end ####################
# Get reducedDim
reduced_dim <- reducedDim(tse, dimred)
Expand All @@ -276,23 +289,30 @@ setMethod("plotRDA", signature = c(x = "matrix"),
# Only 2 dimensions are supported currently
ncomponents <- 2

# If specified, get explained variance
if( add.expl.var ){
# If user wants to add these, we have to get them from the actual RDA
# object. Check if it is found
if( add.expl.var || add.vectors || add.centroids || add.species ){
# Check if data is available
ind <- names(attributes(reduced_dim)) %in% c("rda", "cca", "obj")
# If it can be found
if( any(ind) ){
# Add explained variance
rda <- attributes(reduced_dim)[ind][[1]]
expl_var <- summary(rda)$concont$importance[2, ]*100
} else{
# If it cannot be found, give warning
warning(
paste("RDA/CCA object was not found. Please compute",
"RDA/CCA by using addCCA or getCCA."), call. = FALSE)
warning("RDA/CCA object was not found. Please compute",
"RDA/CCA by using addCCA or getCCA.", call. = FALSE)
# Disable these options if the object was not found
add.expl.var <- add.vectors <- add.centroids <- add.species <-
FALSE
}
}

# If specified, get explained variance
if( add.expl.var ){
expl_var <- summary(rda)$concont$importance[2, ]*100
}

# Get scatter plot with plotReducedDim --> keep theme similar between
# ordination methods
plot <- plotReducedDim(
Expand All @@ -311,21 +331,9 @@ setMethod("plotRDA", signature = c(x = "matrix"),
# Get data for vectors
vector_data <- NULL
if( add.vectors ){
# Check if data is available
ind <- names(attributes(reduced_dim)) %in% c("rda", "cca", "obj")
# If it can be found
if( any(ind) ){
# Get biplot from cca object
rda <- attributes(reduced_dim)[ind][[1]]
vector_data <- rda$CCA$biplot
vector_data <- as.data.frame(vector_data)
vector_data[["group"]] <- rownames(vector_data)
} else{
# If it cannot be found, give warning
warning(
paste("RDA/CCA object was not found. Please compute RDA/CCA",
"by using addCCA or getCCA."), call. = FALSE)
}
vector_data <- rda$CCA$biplot
vector_data <- as.data.frame(vector_data)
vector_data[["group"]] <- rownames(vector_data)
}

# Get variable names from sample metadata
Expand All @@ -334,15 +342,14 @@ setMethod("plotRDA", signature = c(x = "matrix"),
# Check if variable names can be found metadata
all_var_found <- FALSE
if( !is.null(vector_data) && length(variable_names) > 0 ){
all_var_found <- all(colSums(
sapply(rownames(vector_data), function(x)
sapply(variable_names, function(y) grepl(y, x)) )) == 1)
all_var_found <- vapply(rownames(vector_data), function(x)
vapply(variable_names, function(y) grepl(y, x), logical(1L)),
logical(ncol(coldata)) )
all_var_found <- all( colSums(all_var_found) == 1)
}

# Get vector labels
if( !is.null(vector_data) ){
# Get those names that are present in data

# If user has not provided vector labels
if( is.null(vec.lab) ){
vector_label <- rownames(vector_data)
Expand Down Expand Up @@ -387,17 +394,32 @@ setMethod("plotRDA", signature = c(x = "matrix"),
vector_data[["vector_label"]] <- vector_label
} else{
# If it cannot be found, give warning
warning(
paste("Significance data was not found. please compute",
"CCA/RDA by using addCCA or getCCA."), call. = FALSE)
warning("Significance data was not found. please compute",
"CCA/RDA by using addCCA or getCCA.", call. = FALSE)
}
}

# If user wants to add site scores
centroids <- NULL
if( add.centroids ){
.require_package("vegan")
centroids <- vegan::scores(rda, display = "cn") |> as.data.frame()
colnames(centroids) <- c("x", "y")
}

# If user wants to add species scores
species_scores <- NULL
if( add.species ){
species_scores <- scores(rda, display = "species") |> as.data.frame()
colnames(species_scores) <- c("x", "y")
}
# Create a list to return
result <- list(
plot = plot,
ellipse_data = ellipse_data,
vector_data = vector_data
vector_data = vector_data,
centroids = centroids,
species_scores = species_scores
)
return(result)
}
Expand All @@ -409,9 +431,10 @@ setMethod("plotRDA", signature = c(x = "matrix"),
# Get variable names from sample metadata
var_names <- colnames(coldata)
# Loop through vector labels
vector_label <- sapply(vector_label, FUN = function(name){
vector_label <- lapply(vector_label, FUN = function(name){
# Get the real variable name from sample metadata
var_name <- var_names[ sapply(var_names, function(x) grepl(x, name)) ]
var_name <- var_names[
unlist(lapply(var_names, function(x) grepl(x, name))) ]
# If the vector label includes also group name
if( !name %in% var_names ){
# Get the group name
Expand All @@ -426,14 +449,15 @@ setMethod("plotRDA", signature = c(x = "matrix"),
# Replace underscores with space
new_name <- gsub("_", repl.underscore, new_name)
return(new_name)
})
}) |> unlist()
return(vector_label)
}

# This function adds significance info to vector labels
.add_signif_to_vector_labels <- function(
vector_label, var_names, signif_data, repl.underscore = " ", ...){
# Replace underscores from significance data and variable names to match labels
# Replace underscores from significance data and variable names to match
# labels
rownames(signif_data) <- lapply(
rownames(signif_data), function(x) gsub("_", repl.underscore, x)
) |> unlist()
Expand All @@ -443,7 +467,8 @@ setMethod("plotRDA", signature = c(x = "matrix"),
# Loop through vector labels
vector_label <- lapply(vector_label, FUN = function(name){
# Get the real variable name from sample metadata
var_name <- var_names[ sapply(var_names, function(x) grepl(x, name)) ]
var_name <- var_names[
unlist(lapply(var_names, function(x) grepl(x, name))) ]
# Add percentage how much this variable explains, and p-value
new_name <- expr(paste(!!name, " (",
!!format(round(signif_data[var_name, "Explained variance"]*100, 1),
Expand Down Expand Up @@ -606,5 +631,23 @@ setMethod("plotRDA", signature = c(x = "matrix"),
}
}
}

# If user wants to add centroids
if( !is.null(plot_data[["centroids"]]) ){
plot <- plot +
geom_point(
plot_data[["centroids"]],
mapping = aes(x = x, y = y),
shape = 10, color = "blue")
}

# If user wants to add species scores
if( !is.null(plot_data[["species_scores"]]) ){
plot <- plot + geom_point(
plot_data[["species_scores"]],
mapping = aes(x = x, y = y),
shape = 4, color = "red")
}

return(plot)
}
6 changes: 6 additions & 0 deletions man/plotCCA.Rd
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