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R/registerAppOptions.R changed.

Newly tracked file

100.00% 100.00% ø

R/utils_tooltip.R created.

83.16% 100.00% -0.28%

R/family_RowDotPlot.R changed.

83.27% 100.00% -0.27%

R/family_ColumnDotPlot.R changed.

Other files ignored by Codecov

NEWS.md has changed.

tests/testthat/test_hover.R has changed.

man/registerAppOptions.Rd has changed.

DESCRIPTION has changed.

@@ -35,6 +35,7 @@

#' Defaults to 100.}
#' \item{\code{RowTable.select.details}}{A function that takes a string containing the name of a feature (i.e., the current selection in the \linkS4class{RowTable}) and returns a HTML element with more details.} 
#' \item{\code{ColumnTable.select.details}}{A function that takes a string containing the name of a sample (i.e., the current selection in the \linkS4class{ColumnTable}) and returns a HTML element with more details.}
#' \item{\code{tooltip.signif}}{Number of \emph{significant} digits to display in the tooltip. Defaults to 6.}
#' }
#'
#' The registered options are stored in the SummarizedExperiment to ensure that we can recover the application state with the combination of the SummarizedExperiment and list of Panel settings.

@@ -0,0 +1,50 @@

1	+	#' Generate Text in Tooltip
2	+	#'
3	+	#' @param name Identifier of the data point.
4	+	#' Typically, from the \code{rownames} or \code{colnames}.
5	+	#' @param fields Named list of fields to include in the tooltip text.
6	+	#' See \emph{Details}.
7	+	#' @param value Scalar representing one value in \code{fields}.
8	+	#'
9	+	#' @details
10	+	#' Every item in the argument \code{fields} is added as a separate line in the tooltip.
11	+	#' The line is formatted as \dQuote{\bold{name:} value}.
12	+	#'
13	+	#' @return
14	+	#' \code{.generate_tooltip_html} returns an \code{\link{HTML}} element
15	+	#' that will be displayed in the tooltip.
16	+	#'
17	+	#' \code{.process_tooltip_field} converts individual fields to a character
18	+	#' representation suitable for display. For instance, this may include trimming
19	+	#' double-precision scalars to a set number of significant digits.
20	+	#'
21	+	#' @author Kevin Rue-Albrecht
22	+	#'
23	+	#' @rdname INTERNAL_generate_tooltip_html
24	+	.generate_tooltip_html <- function(name, fields) {
25	+	fields <- sapply(fields, function(x) .process_tooltip_field(x), USE.NAMES = TRUE)
26	+	HTML(
27	+	paste0(c(
28	+	sprintf("<strong>%s</strong>", name),
29	+	sprintf("%s: <i>%s</i>", names(fields), fields)
30	+	), collapse = "<br />")
31	+	)
32	+	}
33	+
34	+	#' @rdname INTERNAL_generate_tooltip_html
35	+	.process_tooltip_field <- function(value) {
36	+	original <- value
37	+	if (is.double(value)) {
38	+	value <- signif(value, digits = getAppOption("tooltip.signif", default = 6))
39	+	value <- ifelse(
40	+	identical(value, original),
41	+	as.character(value),
42	+	paste0(as.character(value), "(...)")
43	+	)
44	+	} else if (is.factor(value)) {
45	+	value <- as.character(value)
46	+	} else {
47	+	value <- as.character(value)
48	+	}
49	+	value
50	+	}

@@ -600,15 +600,9 @@


setMethod(".getTooltipUI", "RowDotPlot", function(x, se, name) {
    if (length(x[[.tooltipRowData]]) > 0) {
        # as.data.frame sometimes needed to fix names of items in vector
        info <- as.data.frame(rowData(se)[name, x[[.tooltipRowData]], drop=FALSE])
        info <- sapply(info, function(x) as.character(x))
        ui <- HTML(
            paste0(c(
                sprintf("<strong>%s</strong>", name),
                sprintf("%s: %s", names(info), info)
                ), collapse = "<br />")
            )
        # as.data.frame sometimes needed before as.list to fix names of items in vector
        info <- as.list(as.data.frame(rowData(se)[name, x[[.tooltipRowData]], drop=FALSE]))
        ui <- .generate_tooltip_html(name, info)
        ui
    } else {
        name

@@ -603,15 +603,9 @@


setMethod(".getTooltipUI", "ColumnDotPlot", function(x, se, name) {
    if (length(x[[.tooltipColData]]) > 0) {
        # as.data.frame sometimes needed to fix names of items in vector
        info <- as.data.frame(colData(se)[name, x[[.tooltipColData]], drop=FALSE])
        info <- sapply(info, function(x) as.character(x))
        ui <- HTML(
            paste0(c(
                sprintf("<strong>%s</strong>", name),
                sprintf("%s: %s", names(info), info)
                ), collapse = "<br />")
            )
        # as.data.frame sometimes needed before as.list to fix names of items in vector
        info <- as.list(as.data.frame(colData(se)[name, x[[.tooltipColData]], drop=FALSE]))
        ui <- .generate_tooltip_html(name, info)
        ui
    } else {
        name

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New file R/utils_tooltip.R

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89.56% 100.00% +0.01%

regulate the number of significant digits shown in the tooltip (#604)

kevinrue

e3a3ffa

CI Passed

+1 Files

89.54% ø ø

Export constants used in iSEEu (#603)

kevinrue

c9a4b48

CI Passed

Files		•	•	•	Coverage
R	+7	+7	ø	ø	^0.01% 89.56%
Project Totals (70 files)	5,527	4,950	0	577	89.56%

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Compare `c9a4b48 ... +0 ... e3a3ffa`

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2 Commits

35	35		#' Defaults to 100.}
36	36		#' \item{\code{RowTable.select.details}}{A function that takes a string containing the name of a feature (i.e., the current selection in the \linkS4class{RowTable}) and returns a HTML element with more details.}
37	37		#' \item{\code{ColumnTable.select.details}}{A function that takes a string containing the name of a sample (i.e., the current selection in the \linkS4class{ColumnTable}) and returns a HTML element with more details.}
	38	+	#' \item{\code{tooltip.signif}}{Number of \emph{significant} digits to display in the tooltip. Defaults to 6.}
38	39		#' }
39	40		#'
40	41		#' The registered options are stored in the SummarizedExperiment to ensure that we can recover the application state with the combination of the SummarizedExperiment and list of Panel settings.

600	600
601	601		setMethod(".getTooltipUI", "RowDotPlot", function(x, se, name) {
602	602		if (length(x[[.tooltipRowData]]) > 0) {
603		-	# as.data.frame sometimes needed to fix names of items in vector
604		-	info <- as.data.frame(rowData(se)[name, x[[.tooltipRowData]], drop=FALSE])
605		-	info <- sapply(info, function(x) as.character(x))
606		-	ui <- HTML(
607		-	paste0(c(
608		-	sprintf("<strong>%s</strong>", name),
609		-	sprintf("%s: %s", names(info), info)
610		-	), collapse = "<br />")
611		-	)
	603	+	# as.data.frame sometimes needed before as.list to fix names of items in vector
	604	+	info <- as.list(as.data.frame(rowData(se)[name, x[[.tooltipRowData]], drop=FALSE]))
	605	+	ui <- .generate_tooltip_html(name, info)
612	606		ui
613	607		} else {
614	608		name

603	603
604	604		setMethod(".getTooltipUI", "ColumnDotPlot", function(x, se, name) {
605	605		if (length(x[[.tooltipColData]]) > 0) {
606		-	# as.data.frame sometimes needed to fix names of items in vector
607		-	info <- as.data.frame(colData(se)[name, x[[.tooltipColData]], drop=FALSE])
608		-	info <- sapply(info, function(x) as.character(x))
609		-	ui <- HTML(
610		-	paste0(c(
611		-	sprintf("<strong>%s</strong>", name),
612		-	sprintf("%s: %s", names(info), info)
613		-	), collapse = "<br />")
614		-	)
	606	+	# as.data.frame sometimes needed before as.list to fix names of items in vector
	607	+	info <- as.list(as.data.frame(colData(se)[name, x[[.tooltipColData]], drop=FALSE]))
	608	+	ui <- .generate_tooltip_html(name, info)
615	609		ui
616	610		} else {
617	611		name

Compare c9a4b48 ... +0 ... e3a3ffa

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Compare `c9a4b48 ... +0 ... e3a3ffa`