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Update fxn parameters
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Signed-off-by: Daena Rys <[email protected]>
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@Daenarys8
Daenarys8 committed Jun 3, 2024
1 parent a137806 commit 054a7f6
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Showing 27 changed files with 1,834 additions and 1,531 deletions.
224 changes: 119 additions & 105 deletions R/plotAbundance.R
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235 changes: 123 additions & 112 deletions R/plotAbundanceDensity.R
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68 changes: 34 additions & 34 deletions R/plotCCA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
#' output of \code{\link[mia:runCCA]{CCA and RDA}} functions, two common methods
#' for supervised ordination of microbiome data.
#'
#' @param object a
#' @param x a
#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}
#' or a matrix of weights. The latter is returned as output from \code{\link[mia:runCCA]{calculateRDA}}.
#'
Expand Down Expand Up @@ -112,26 +112,26 @@
#'
#' # Create RDA plot coloured by variable
#' plotRDA(tse, "RDA",
#' colour_by = "ClinicalStatus")
#' colour.by = "ClinicalStatus")
#'
#' # Create RDA plot with empty ellipses
#' plotRDA(tse, "RDA",
#' colour_by = "ClinicalStatus",
#' colour.by = "ClinicalStatus",
#' add.ellipse = "colour")
#'
#' # Create RDA plot with text encased in labels
#' plotRDA(tse, "RDA",
#' colour_by = "ClinicalStatus",
#' colour.by = "ClinicalStatus",
#' vec.text = FALSE)
#'
#' # Create RDA plot without repelling text
#' plotRDA(tse, "RDA",
#' colour_by = "ClinicalStatus",
#' colour.by = "ClinicalStatus",
#' repel.labels = FALSE)
#'
#' # Create RDA plot without vectors
#' plotRDA(tse, "RDA",
#' colour_by = "ClinicalStatus",
#' colour.by = "ClinicalStatus",
#' add.vectors = FALSE)
#'
#' # Calculate RDA as a separate object
Expand All @@ -148,40 +148,40 @@ NULL
#' @rdname plotCCA
#' @aliases plotRDA
#' @export
setGeneric("plotCCA", signature = c("object"),
function(object, ...) standardGeneric("plotCCA"))
setGeneric("plotCCA", signature = c("x"),
function(x, ...) standardGeneric("plotCCA"))

#' @rdname plotCCA
#' @aliases plotRDA
#' @export
setMethod("plotCCA", signature = c(object = "SingleCellExperiment"),
function(object, dimred, ...){
setMethod("plotCCA", signature = c(x = "SingleCellExperiment"),
function(x, dimred, ...){
# Reproduce plotRDA function
return(plotRDA(object, dimred, ...))
return(plotRDA(x, dimred, ...))
}
)

#' @rdname plotCCA
#' @aliases plotRDA
#' @export
setMethod("plotCCA", signature = c(object = "matrix"),
function(object, ...){
setMethod("plotCCA", signature = c(x = "matrix"),
function(x, ...){
# Reproduce plotRDA function
return(plotRDA(object, ...))
return(plotRDA(x, ...))
}
)

#' @rdname plotCCA
#' @aliases plotCCA
#' @export
setGeneric("plotRDA", signature = c("object"),
function(object, ...) standardGeneric("plotRDA"))
setGeneric("plotRDA", signature = c("x"),
function(x, ...) standardGeneric("plotRDA"))

#' @rdname plotCCA
#' @aliases plotCCA
#' @export
setMethod("plotRDA", signature = c(object = "SingleCellExperiment"),
function(object, dimred,
setMethod("plotRDA", signature = c(x = "SingleCellExperiment"),
function(x, dimred,
add.ellipse = TRUE, ellipse.alpha = 0.2, ellipse.linewidth = 0.1, ellipse.linetype = 1,
confidence.level = 0.95, vec.size = 0.5, vec.color = vec.colour, vec.colour = "black", vec.linetype = 1,
arrow.size = 0.25, label.color = label.colour, label.colour = "black", label.size = 4,
Expand Down Expand Up @@ -255,7 +255,7 @@ setMethod("plotRDA", signature = c(object = "SingleCellExperiment"),
###################### Input check end ####################
# Get data for plotting
plot_data <- .incorporate_rda_vis(
object, dimred, sep.group = sep.group, repl.underscore = repl.underscore,
x, dimred, sep.group = sep.group, repl.underscore = repl.underscore,
add.significance = add.significance, add.expl.var = add.expl.var,
add.ellipse = add.ellipse, add.vectors = add.vectors, ...
)
Expand All @@ -275,33 +275,33 @@ setMethod("plotRDA", signature = c(object = "SingleCellExperiment"),
#' @rdname plotCCA
#' @aliases plotCCA
#' @export
setMethod("plotRDA", signature = c(object = "matrix"),
function(object, ...){
setMethod("plotRDA", signature = c(x = "matrix"),
function(x, ...){
# Construct TreeSE from rda/cca object
object <- .rda2tse(object)
x <- .rda2tse(x)
# Run plotRDA method for TreeSE
return(plotRDA(object, "RDA", ...))
return(plotRDA(x, "RDA", ...))
}
)


################## HELP FUNCTIONS ##########################

# Construct TreeSE from rda/cca object to pass it to downstream functions
.rda2tse <- function(object) {
.rda2tse <- function(x) {
# Convert rda/cca object to TreeSE
object <- TreeSummarizedExperiment(
assays = matrix(ncol = nrow(object), dimnames = list(NULL, rownames(object))),
reducedDims = list(RDA = object)
x <- TreeSummarizedExperiment(
assays = matrix(ncol = nrow(x), dimnames = list(NULL, rownames(x))),
reducedDims = list(RDA = x)
)
return(object)
return(x)
}

# Get data for plotting
#' @importFrom scater plotReducedDim retrieveCellInfo
#' @importFrom SingleCellExperiment reducedDim reducedDimNames
.incorporate_rda_vis <- function(
tse, dimred, ncomponents = 2, colour_by = color_by, color_by = NULL,
tse, dimred, ncomponents = 2, colour.by = color_by, color_by = NULL,
add.significance = TRUE, add.expl.var = TRUE, add.ellipse = TRUE,
add.vectors = TRUE, vec.lab = NULL, expl_var = NULL,
sep.group = "\U2012", repl.underscore = " ", ...){
Expand Down Expand Up @@ -338,16 +338,16 @@ setMethod("plotRDA", signature = c(object = "matrix"),

# Get scatter plot with plotReducedDim --> keep theme similar between ordination methods
plot <- plotReducedDim(
tse, dimred = dimred, ncomponents = ncomponents, colour_by = colour_by,
tse, dimred = dimred, ncomponents = ncomponents, colour.by = colour.by,
percentVar = expl_var, ...)

# Get data for ellipse
ellipse_data <- NULL
if( add.ellipse != FALSE && !is.null(colour_by) ){
if( add.ellipse != FALSE && !is.null(colour.by) ){
ellipse_data <- reduced_dim
ellipse_data <- as.data.frame(ellipse_data)
ellipse_data[[colour_by]] <- retrieveCellInfo(tse, colour_by)[["value"]]
attributes(ellipse_data)$colour_by <- colour_by
ellipse_data[[colour.by]] <- retrieveCellInfo(tse, colour.by)[["value"]]
attributes(ellipse_data)$colour.by <- colour.by
}

# Get data for vectors
Expand Down Expand Up @@ -514,7 +514,7 @@ setMethod("plotRDA", signature = c(object = "matrix"),
data <- plot_data$ellipse_data
xvar <- colnames(data)[[1]]
yvar <- colnames(data)[[2]]
colour_var <- attributes(plot_data$ellipse_data)$colour_by
colour_var <- attributes(plot_data$ellipse_data)$colour.by
# Add ellipses to plot (fill or colour the edge)
if( add.ellipse %in% c(TRUE, "fill") ){
plot <- plot +
Expand Down
10 changes: 5 additions & 5 deletions R/plotColTile.R
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Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,7 @@ setMethod("plotRowTile", signature = c("SummarizedExperiment"),
tile_data <- .summarise_tile_data(object,
tile_data,
type)
tile_data$colour_by <- tile_data$Y
tile_data$colour.by <- tile_data$Y
.tile_plotter(tile_data,
xlab = xlab,
ylab = ylab,
Expand All @@ -145,15 +145,15 @@ setMethod("plotRowTile", signature = c("SummarizedExperiment"),
}

.tile_plotter <- function(data,
add_legend = TRUE,
add.legend = TRUE,
xlab,
ylab,
rect_alpha = 1,
rect_colour = "black",
na.value = "grey80"){
coord <- .get_xcoord_mid(data)
# get plotting arguments for rect
rect_args <- .get_rect_args(colour_by = ylab,
rect_args <- .get_rect_args(colour.by = ylab,
alpha = rect_alpha,
colour = rect_colour)
rect_args$args$mapping$xmin <- sym("xmin")
Expand All @@ -177,14 +177,14 @@ setMethod("plotRowTile", signature = c("SummarizedExperiment"),
breaks = seq(0,1,0.1))
# resolve the fill colours
plot_out <- .resolve_plot_colours(plot_out,
data$colour_by,
data$colour.by,
ylab,
fill = TRUE,
na.value = na.value)
# add legend and theme
plot_out <- plot_out +
theme_classic()
if (!add_legend) {
if (!add.legend) {
plot_out <- plot_out + theme(legend.position = "none")
}
plot_out
Expand Down
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