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Improved package vignette (Getting Started) for pkgdown #3

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Sep 19, 2023
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6 changes: 3 additions & 3 deletions R/boxplotSubarray.R
Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,13 @@
#' [read_adat()].
#' @param color.by A column name to color the subarrays by. Typically a meta
#' data field in the adat such as `SlideId`.
#' @param labels Character. A column name of `adat` used to label each box.
#' @param labels Character. A column name of `.data` used to label each box.
#' @param do.log Logical. Should the data should be log10-transformed?
#' @param y.lim Numeric. Length 2. The upper- and lower-quantiles of the
#' _total_ data used to determine the y-axis limits of the plot.
#' If `NULL`, all points are shown.
#' @param apts An optional subset of analytes (as `AptNames`) to add on top
#' of subarray boxplot.
#' @param apts Optional. A subset of analytes (as `AptNames`) to add as points
#' on top of the subarray boxplot.
#' @author Stu Field
#' @seealso [geom_boxplot()]
#' @examples
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3 changes: 1 addition & 2 deletions R/plotPDFbyGroup.R
Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,7 @@ plotPDFbyGroup <- function(data, apt, group.var, cols, xlim = NULL,
p <- data |>
dplyr::select(!!group.var, apt) |>
.refactorData() |> # this is about ghost levels
ggplot(aes(x = !!sym(apt),
color = !!group.var)) +
ggplot(aes(x = !!sym(apt), color = !!group.var)) +
geom_density(aes(fill = !!group_var),
alpha = ifelse(fill, 0.2, 1),
linewidth = ifelse(fill, 0.1, 0.75),
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4 changes: 1 addition & 3 deletions R/plotVolcanoHTML.R
Original file line number Diff line number Diff line change
Expand Up @@ -93,9 +93,7 @@ plotVolcanoHTML.default <- function(data, ...) {
#' variable name in `data` for the Target Names.
#' @importFrom SomaDataIO rn2col col2rn
#' @export
plotVolcanoHTML.data.frame <- function(data,
FC = signed.log2.fold.change,
p.vec = p.value,
plotVolcanoHTML.data.frame <- function(data, FC = signed.log2.fold.change, p.vec = p.value,
cutoff = 0.05 / nrow(data),
fc.cutoff = 1,
main = NULL, x.lab = NULL,
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9 changes: 3 additions & 6 deletions R/utils.R
Original file line number Diff line number Diff line change
Expand Up @@ -54,13 +54,10 @@
for ( meta in nms ) {
levs <- levels(data[[meta]])
data[[meta]] <- droplevels(data[[meta]])
if ( interactive() ) {
levs2 <- levels(data[[meta]])
sdiff <- setdiff(levs, levels(data[[meta]]))
if ( length(sdiff) > 0L && interactive() ) {
.info(
paste("Dropping levels",
value(setdiff(levs, levs2)),
"from",
value(meta))
paste("Dropping levels", value(sdiff), "from", value(meta))
)
}
}
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6 changes: 3 additions & 3 deletions man/boxplotSubarray.Rd

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