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plotRDA fix #101

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merged 4 commits into from
Oct 15, 2023
Merged

plotRDA fix #101

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TuomasBorman Oct 14, 2023
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TuomasBorman Oct 14, 2023
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TuomasBorman Oct 14, 2023
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TuomasBorman Oct 14, 2023
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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: 1.9.3
Version: 1.9.4
Authors@R:
c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
email = "[email protected]",
Expand Down
90 changes: 34 additions & 56 deletions R/plotCCA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -296,11 +296,9 @@ setMethod("plotRDA", signature = c(object = "matrix"),
#' @importFrom SingleCellExperiment reducedDim reducedDimNames
.incorporate_rda_vis <- function(
tse, dimred, ncomponents = 2, colour_by = color_by, color_by = NULL,
shape_by = NULL, size_by = NULL, order_by = NULL, text_by = NULL,
other_fields = list(), swap_rownames = NULL, point.padding = NA,
add.ellipse = TRUE, add.vectors = TRUE, add.significance = TRUE,
add.expl.var = TRUE, vec_lab = NULL, bins = NULL, sep.group = "\U2012",
repl.underscore = " ", ...){
add.significance = TRUE, add.expl.var = TRUE, add.ellipse = TRUE,
add.vectors = TRUE, vec.lab = NULL, expl_var = NULL,
sep.group = "\U2012", repl.underscore = " ", ...){

# Check dimred
if( !dimred %in% reducedDimNames(tse) ){
Expand All @@ -312,32 +310,30 @@ setMethod("plotRDA", signature = c(object = "matrix"),
if( ncol(reduced_dim) < 2 ){
stop("reducedDim specified by 'dimred' must have at least 2 columns.", call. = FALSE)
}
# Check that each by-argument matches the name of a column in colData
by_args <- c(
colour_by = colour_by,
shape_by = shape_by,
size_by = size_by,
order_by = order_by,
text_by = text_by
)
correct_args <- sapply(by_args, function(x) x %in% names(colData(tse)))
sapply(names(by_args[!correct_args]),
function(x) {
stop(paste0("'", x, "' must match the name of a column in colData."),
call. = FALSE)
})
# Only 2 dimensions are supported currently
ncomponents <- 2
# Make list of arguments for plotReducedDim
plotReducedDim_args <- c(by_args, list(
object = tse, dimred = dimred, ncomponents = ncomponents,
text_size = 5, text_colour = "black", text_color = "black",
label_format = c("%s %i", " (%i%%)"), other_fields = other_fields,
swap_rownames = swap_rownames, point.padding = point.padding, force = 1,
rasterise = FALSE, scattermore = FALSE, summary_fun = "sum", hex = FALSE
))

# If specified, get explained variance
if( add.expl.var ){
# Check if data is available
ind <- names(attributes(reduced_dim)) %in% c("rda", "cca")
# 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 runCCA or calculateCCA."),
call. = FALSE)
}
}

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

# Get data for ellipse
ellipse_data <- NULL
Expand Down Expand Up @@ -384,7 +380,7 @@ setMethod("plotRDA", signature = c(object = "matrix"),
# Get those names that are present in data

# If user has not provided vector labels
if( is.null(vec_lab) ){
if( is.null(vec.lab) ){
vector_label <- rownames(vector_data)
# Make labels more tidy
if( all_var_found ){
Expand All @@ -398,12 +394,12 @@ setMethod("plotRDA", signature = c(object = "matrix"),
vector_data$vector_label <- vector_label
} else{
# Check that user-provided labels are correct length
if( length(vec_lab) != nrow(vector_data) ){
if( length(vec.lab) != nrow(vector_data) ){
stop("Number of labels in 'vec_lab' do not match with number of vectors.",
call. = FALSE)
}
# If they are, add labels to data
vector_data$vector_label <- vec_lab
vector_data$vector_label <- vec.lab
}
}

Expand All @@ -422,7 +418,8 @@ setMethod("plotRDA", signature = c(object = "matrix"),
# Get vector labels
vector_label <- vector_data[["vector_label"]]
# Add significance to vector labels
vector_label <- .add_signif_to_vector_labels(vector_label, variable_names, signif_data, ...)
vector_label <- .add_signif_to_vector_labels(
vector_label, variable_names, signif_data, repl.underscore)
vector_data[["vector_label"]] <- vector_label
} else{
# If it cannot be found, give warning
Expand All @@ -435,26 +432,6 @@ setMethod("plotRDA", signature = c(object = "matrix"),
# Create labels for axis
xlab <- paste0(dimred, " 1")
ylab <- paste0(dimred, " 2")
if( add.expl.var ){
# Check if data is available
ind <- names(attributes(reduced_dim)) %in% c("rda", "cca")
# If it can be found
if( any(ind) ){
# Add explained variance
rda <- attributes(reduced_dim)[ind][[1]]
xlab <- paste0(
xlab, " (",
format(round( summary(rda)$concont$importance[2, 1]*100, 1 ), nsmall = 1 ), "%)")
ylab <- paste0(
ylab, " (",
format(round( summary(rda)$concont$importance[2, 2]*100, 1 ), nsmall = 1 ), "%)")
} else{
# If it cannot be found, give warning
warning(paste("RDA/CCA object was not found. Please compute",
"RDA/CCA by using runCCA or calculateCCA."),
call. = FALSE)
}
}

# Create a list to return
result <- list(
Expand All @@ -470,7 +447,7 @@ setMethod("plotRDA", signature = c(object = "matrix"),
# Make vector labels more tidy, i.e, separate variable and group names.
# Replace also underscores with space
.tidy_vector_labels <- function(
vector_label, coldata, sep.group = "\U2012", repl.underscore = " "){
vector_label, coldata, sep.group = "\U2012", repl.underscore = " ", ...){
# Get variable names from sample metadata
var_names <- colnames(coldata)
# Loop through vector labels
Expand All @@ -495,7 +472,8 @@ setMethod("plotRDA", signature = c(object = "matrix"),
}

# This function adds significance info to vector labels
.add_signif_to_vector_labels <- function(vector_label, var_names, signif_data, repl.underscore = " ", ...){
.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
rownames(signif_data) <- sapply(rownames(signif_data), function(x) gsub("_", repl.underscore, x))
var_names <- sapply(var_names, function(x) gsub("_", repl.underscore, x))
Expand All @@ -508,7 +486,7 @@ setMethod("plotRDA", signature = c(object = "matrix"),
paste(!!name, " (",
!!format(
round( signif_data[var_name, "Explained variance"]*100, 1),
nsmall = 1), "%, P = ",
nsmall = 1), "%, ", italic("P"), " = ",
!!gsub("0\\.","\\.", format(
round( signif_data[var_name, "Pr(>F)"], 3),
nsmall = 3)), ")"))
Expand Down Expand Up @@ -609,4 +587,4 @@ setMethod("plotRDA", signature = c(object = "matrix"),
# Add axis labels
plot <- plot + xlab(plot_data$xlab) + ylab(plot_data$ylab)
return(plot)
}
}
6 changes: 2 additions & 4 deletions tests/testthat/test-plotCCA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ test_that("plot RDA/CCA", {
expect_no_error(plotRDA(tse, "RDA"))

# Wrong-entry scenarios
expect_error(plotRDA(tse, "RDA", colour_by = "wrong colname"),
"'colour_by' must match the name of a column in colData.")
expect_error(plotRDA(tse, "RDA", colour_by = "cohort", shape_by = "wrong colname"),
"'shape_by' must match the name of a column in colData.")
expect_error(plotRDA(tse, "RDA", colour_by = "wrong colname"))
expect_error(plotRDA(tse, "RDA", colour_by = "cohort", shape_by = "wrong colname"))
expect_error(plotRDA(tse, "RDA", add.ellipse = "invalid value"),
"'add.ellipse' must be one of c(TRUE, FALSE, 'fill', 'color', 'colour').",
fixed = TRUE)
Expand Down
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