#' Dimensionality reduction through PCA
#'
#' @param MAE A multi-assay experiment object
#' @param tax_level The taxon level used for organisms
#' @param color A condition to color data points by e.g. "AGE"
#' @param shape A condition to shape data points by e.g. "SEX"
#' @param pcx Principal component on the x-axis e.g. 1
#' @param pcy Principal component on the y-axis e.g. 2
#' @param pcz Principal component on the z-axis e.g. 3
#' @param datatype Datatype to use e.g. c("logcpm", "relabu", "counts")
#' @return A list with a plotly object and summary table
#'
#' @examples
#' data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
#' toy_data <- readRDS(data_dir)
#' result <- dimred_pca(toy_data,
#' tax_level = "genus",
#' color = "AGE",
#' shape = "DISEASE",
#' pcx = 1,
#' pcy = 2,
#' datatype = "logcpm"
#' )
#' result$plot
#' result$table
#'
#' @import dplyr
#' @import scales
#' @import plotly
#' @import magrittr
#' @import reshape2
#' @import MultiAssayExperiment
#'
#' @export
dimred_pca <- function(MAE,
tax_level,
color,
shape = NULL,
pcx = 1,
pcy = 2,
pcz = NULL,
datatype = c("logcpm", "relabu", "counts")) {
# Default variables
datatype <- match.arg(datatype)
# Extract data
microbe <- MAE[["MicrobeGenetics"]]
# host <- MultiAssayExperiment::experiments(MAE)[[2]]
tax_table <- as.data.frame(rowData(microbe)) # organism x taxlev
sam_table <- as.data.frame(colData(microbe)) # sample x condition
counts_table <-
as.data.frame(assays(microbe))[, rownames(sam_table)] #organism x sample
df <- counts_table %>%
# Sum counts by taxon level
upsample_counts(tax_table, tax_level) %>%
# Choose data type
{
if (datatype == "relabu") {
counts_to_relabu(.)
} else if (datatype == "logcpm") {
counts_to_logcpm(.)
} else {
.
}
} %>%
# Fix constant/zero row
{
if (sum(base::rowSums(as.matrix(.)) == 0) > 0) {
. <- .[-which(base::rowSums(as.matrix(.)) == 0), ]
} else {
.
}
} %>%
# Transpose
t()
# PCA
df.prcomp <- stats::prcomp(df, scale = TRUE)
# Principle Components
df.pca <- df.prcomp$x
# Importance
df.imp <- t(summary(df.prcomp)$importance)
# Merge in covariate information
if (!is.null(shape)) {
df.pca.m <- merge(df.pca,
sam_table[, c(color, shape), drop = FALSE],
by = 0, all = TRUE
)
# When shape is required
# Bypass duplicate colnames if color == shape
shape <- colnames(df.pca.m)[ncol(df.pca.m)]
df.pca.m[[shape]] <- as.factor(df.pca.m[[shape]])
} else {
df.pca.m <-
merge(df.pca, sam_table[, color, drop = FALSE], by = 0, all = TRUE)
shape <- "shape" # Referenced by plotly later
df.pca.m[[shape]] <- 1 # Constant results in omitting shape
}
# Plotly | Scatterplot
if (is.null(pcz)) {
# 2D Plot
p <- plot_ly(df.pca.m,
x = as.formula(paste("~PC", pcx, sep = "")),
y = as.formula(paste("~PC", pcy, sep = "")),
mode = "markers",
color = as.formula(paste("~", color, sep = "")),
symbol = as.formula(paste("~", shape, sep = "")),
type = "scatter",
text = df.pca.m$Row.names,
marker = list(size = 10)
)
} else {
# 3D Plot
p <- plot_ly(df.pca.m,
x = as.formula(paste("~PC", pcx, sep = "")),
y = as.formula(paste("~PC", pcy, sep = "")),
z = as.formula(paste("~PC", pcz, sep = "")),
mode = "markers",
color = as.formula(paste("~", color, sep = "")),
symbol = as.formula(paste("~", shape, sep = "")),
symbols = c(
"circle",
"square",
"diamond",
"cross",
"square-open",
"circle-open",
"diamond-open",
"x"
),
type = "scatter3d",
text = df.pca.m$Row.names,
marker = list(size = 6)
)
}
p$p <- NULL # To suppress a shiny warning
# Formatting importance table
colnames(df.imp) <- c(
"Standard Deviation",
"Variance Explained",
"Cumulative Variance"
)
df.imp[, "Standard Deviation"] <- signif(df.imp[, "Standard Deviation"], 3)
# Show variance as a percentage
df.imp[, 2] <- scales::percent(as.numeric(df.imp[, 2]))
df.imp[, 3] <- scales::percent(as.numeric(df.imp[, 3]))
# Reorder
df.imp <- as.data.frame(df.imp)
df.imp$PC <- rownames(df.imp)
df.imp <- df.imp[, c(4, 1, 2, 3)]
return(list(plot = p, table = df.imp))
}
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