R/jamba-kable-coloring.R
In jmw86069/jamba: Jam Base Methods
#' Extend kableExtra colorization of Rmarkdown tables
#'
#' Extend kableExtra colorization of Rmarkdown tables
#'
#' This function extends the `kableExtra` package, and is only
#' available for use if the `kableExtra` package is installed. It is
#' intended to allow specific color assignment of elements in a
#' data.frame, but otherwise uses the `kableExtra` functions to
#' apply those colors.
#'
#' The use case is to provide colorized HTML output for RMarkdown,
#' it has not been tested with other `format` output.
#'
#' The argument `colorSub` accepts:
#'
#' * `character` vector input where
#' names should match column values
#' * `function` that accepts column values and returns a `character`
#' vector of colors of equal length
#' * `list` input where names should match `colnames(df)`, and where
#' each list element should contain either a `character` vector, or
#' `function` as described above.
#'
#' @returns object with class `c("kableExtra", "knitr_kable")` by default
#' when `return_type="kable"`, suitable to render inside an RMarkdown
#' or HTML context. Or returns `data.frame` when `return_type="data.frame"`.
#'
#' @param df `data.frame` input. Note that `kable` input is not supported.
#' @param colorSub one of the following inputs:
#' * `character` vector of R colors, whose names match entries
#' in the `data.frame` which are given these assigned colors
#' * `function` that takes column values as input, and returns
#' a `character` vector with one color per value, using `NA`
#' or `NULL` to indicate `"transparent"`
#' * `list` whose names match `colnames(df)`, where each entry
#' contains either `character` or `function` option as described
#' above. A `character` vector should be named by values expected
#' in each column. A `function` should take column values as input,
#' and return a `character` vector with same length of R colors.
#' @param background_as_tile `logical` default `TRUE`, whether the
#' cell background color will appear as a rounded tile (`TRUE`)
#' or a rectangle (`FALSE`).
#' Either way, the color does not fill the entire whitespace
#' of the table cell, but only around the text itself.
#' @param color_cells `logical` indicating whether to color individual cells,
#' default `TRUE`. This may be `FALSE` when also applying `row_color_by`,
#' so the entire row will be colorized.
#' @param row_color_by `character` vector with one or more `colnames`,
#' indicating how to colorize entire rows of a table.
#' When one column is defined, colors in `colorSub` are used as normal.
#' When multiple columns are defined, values from each column are
#' concatenated using `sep` delimiter. Then resulting values are
#' compared with `colorSub`.
#' @param sep `character` delimiter used to combine values in multiple
#' columns when `row_color_by` is supplied and contains multiple
#' `colnames`. The delimited character strings are compared to
#' `colorSub` to assign colors.
#' @param border_left,border_right,extra_css `character` values optionally
#' passed to `kableExtra::column_spec()` as a convenient way to apply
#' borders for each column (`border_left`, `border_right`) or enable
#' or disable word-wrapping by column. Some helpful examples:
#' * `border_left=FALSE`: disables left border
#' * `border_left="1px solid #DDDDDD"`: light gray 1 pixel left border
#' * `border_right=FALSE`: disables right border
#' * `border_right="1px solid #DDDDDD"`: light gray 1 pixel right border
#' * `extra_css=NULL`: disables word-wrap
#' * `extra_css="whitespace: nowrap;"`: enables text word-wrap
#' * when all options above contain only `FALSE` or `NULL`, then
#' `kableExtra::column_spec()` is not applied.
#' @param format `character` passed to `knitr::kable()`, default `"html"`
#' which is the intended format for most scenarios.
#' It can be set to `NULL` to enable auto-detection of the format.
#' @param format.args `list` of arguments passed to `base::format()`
#' intended mainly for `numeric` columns.
#' @param row.names `logical` indicating whether to include `rownames(df)`.
#' When `row.names=NA` the default is to display rownames if they
#' are not `NULL` and not equal to `1:nrow(df)`.
#' @param align `character` passed to `kableExtra::kable()` to define
#' alignment of each column.
#' @param return_type `character` string indicating the type of data
#' to return.
#' * `return_type="kable"`: (default) returns object with class
#' `"kableExtra", "knitr_kable"` suitable for downstream processing.
#' * `return_type="data.frame"`: returns a `data.frame` whose cells
#' contain HTML markup with corresponding colors defined.
#' @param verbose boolean indicating whether to print verbose output.
#' @param ... additional arguments are passed to `kableExtra::kable()`
#' which allows the usual customizations on the initial call.
#'
#' @returns `data.frame` or class with `"kableExtra"` dependent upon the
#' `return_type` argument. Note that even the `data.frame` returned
#' will have colors encoded into each cell using HTML.
#'
#' @examplesIf all(check_pkg_installed(c("circlize", "kableExtra")))
#' new_colorSub <- list(
#' column_A=nameVector(rainbow(5), LETTERS[1:5]),
#' column_B=nameVector(rev(rainbow(5)), LETTERS[1:5]),
#' column_C=circlize::colorRamp2(
#' colors=getColorRamp("Reds", n=6),
#' breaks=0:5 * 1000))
#' testdf <- data.frame(column_A=LETTERS[1:5],
#' row.names=LETTERS[1:5],
#' column_B=LETTERS[1:5],
#' column_C=1:5 * 1000)
#'
#' # kableExtra output with colored tiles inside table cells
#' kdf1 <- kable_coloring(
#' df=testdf,
#' colorSub=new_colorSub)
#' print(class(kdf1));
#' kdf1;
#'
#' # kableExtra output with colored rows
#' kdf2 <- kable_coloring(
#' row_color_by=3,
#' df=testdf,
#' colorSub=new_colorSub)
#' class(kdf2);
#' kdf2;
#'
#' # data.frame output is a regular data.frame with HTML contents
#' kdf3 <- kable_coloring(
#' return_type="data.frame",
#' df=testdf,
#' colorSub=new_colorSub)
#' kdf3;
#'
#' @family jam color functions
#' @family jam practical functions
#'
#' @export
kable_coloring <- function
(df,
colorSub=NULL,
background_as_tile=TRUE,
color_cells=TRUE,
row_color_by=NULL,
sep="_",
border_left="1px solid #DDDDDD",
border_right=FALSE,
extra_css="white-space: nowrap;",
format="html",
format.args=list(
trim=TRUE,
big.mark=","),
row.names=NA,
align=NULL,
return_type=c("kable",
"data.frame"),
verbose=FALSE,
...)
{
## Purpose is to enhance kableExtra by automating some manual steps
## required to colorize text fields in a data.frame
##
## The input is expected to be a data.frame
if (!check_pkg_installed("kableExtra")) {
stop("kable_coloring() requires the kableExtra package.");
}
return_type <- match.arg(return_type);
# keep a non-kable copy for now
df1 <- df;
if (all(is.na(row.names))) {
if (length(rownames(df)) > 0 &&
!all(rownames(df) == seq_len(nrow(df)))) {
row.names <- TRUE;
} else {
row.names <- FALSE;
}
}
if (length(align) == 0 ||
all(is.na(align)) ||
max(nchar(align), na.rm=TRUE) == 0) {
align <- sapply(seq_len(ncol(df1)), function(i){
if (is.numeric(df[[i]])) {
"r"
} else {
"l"
}
})
} else {
if (max(nchar(align)) == 1) {
align <- rep(align,
length.out=ncol(df));
}
}
if (TRUE %in% color_cells) {
for (i in colnames(df)) {
if (length(colorSub) > 0 && is.list(colorSub)) {
# colorSub as color_list, named by colnames(df)
# if ("color_sub" %in% names(attributes(colorSub))) {}
if (i %in% names(colorSub)) {
if (verbose) {
printDebug("kable_coloring(): ",
"colorizing column:",
i,
" using colorSub[[i]].");
}
icolorSub <- colorSub[[i]];
if (is.function(icolorSub)) {
value_colors <- icolorSub(df[[i]])
} else {
value_colors <- icolorSub[as.character(df[[i]])]
}
column_values <- df[[i]];
if (is.numeric(column_values) && length(format.args) > 0) {
column_values <- do.call(base::format,
c(list(x=column_values),
format.args));
}
df[[i]] <- kableExtra::cell_spec(
x=column_values,
background_as_tile=background_as_tile,
color=setTextContrastColor(
rmNA(value_colors,
naValue="transparent")
),
background=rmNA(value_colors,
naValue="transparent"))
}
} else if (any(as.character(df[[i]]) %in% names(colorSub))) {
# colorSub as named character vector
if (verbose) {
printDebug("kable_coloring(): ",
"colorizing column:",
i);
}
df[[i]] <- kableExtra::cell_spec(df[[i]],
background_as_tile=background_as_tile,
color=setTextContrastColor(
rmNA(colorSub[as.character(df[[i]])],
naValue="transparent")
),
background=rmNA(colorSub[as.character(df[[i]])],
naValue="transparent"))
} else {
if (verbose) {
printDebug("kable_coloring(): ",
"No values to colorize in column:",
i,
fgText=c("orange","red"));
}
}
}
}
## Convert to kable
if (return_type %in% "kable" || length(row_color_by) > 0) {
df <- kableExtra::kable_styling(
kableExtra::kable(x=df,
escape=FALSE,
format=format,
format.args=format.args,
align=align,
row.names=row.names,
...))
}
## Optionally color rows using values in a column
if (length(row_color_by) > 0) {
if (verbose) {
printDebug("kable_coloring(): ",
"row_color_by:",
row_color_by);
}
row_color_by_value <- NULL;
row_colors <- NULL;
if (length(row_color_by) == 1) {
# one column defines the colors used, most common usage
if (length(colorSub) > 0) {
if (is.numeric(row_color_by)) {
row_color_by <- colnames(df1)[row_color_by];
}
row_color_by_value <- df1[[as.character(row_color_by)]]
if (is.list(colorSub)) {
# colorSub is a list named by colnames(df)
icolorSub <- colorSub[[row_color_by]];
if (is.function(icolorSub)) {
row_colors <- icolorSub(row_color_by_value);
} else {
row_colors <- icolorSub[row_color_by_value];
}
} else {
# colorSub is a named character vector, or single color function
if (is.function(colorSub)) {
row_colors <- colorSub(row_color_by_value);
} else {
row_colors <- colorSub[row_color_by_value];
}
}
} else {
# colorSub is empty, do nothing
}
} else {
# two or more columns define the colors used
row_color_by_value <- as.character(
pasteByRow(df1[, row_color_by, drop=FALSE],
sep=sep));
if (length(colorSub) > 0) {
if (is.list(colorSub)) {
# look for attributes "color_sub"
if ("color_sub" %in% names(attributes(colorSub))) {
color_sub <- attr(colorSub, "color_sub");
} else {
color_sub <- unlist(unname(
lapply(colorSub, function(icolorSub){
if (is.function(icolorSub)) {
return(character(0))
}
icolorSub
})))
}
row_colors <- rmNA(naValue="transparent",
color_sub[row_color_by_value])
} else {
# colorSub is a named character vector, or single color function
if (is.function(colorSub)) {
row_colors <- colorSub(row_color_by_value);
} else {
row_colors <- colorSub[row_color_by_value];
}
}
}
}
if (verbose) {
printDebug("kable_coloring(): ",
"row_color_by_value:",
row_color_by_value);
printDebug("kable_coloring(): ",
"row_colors:",
row_colors);
}
row_colors_valid <- unique(rmNA(row_colors));
for (row_color in row_colors_valid) {
which_rows <- which(row_colors %in% row_color);
if (verbose) {
printDebug("kable_coloring(): ",
"colorizing rows:",
which_rows,
closestRcolor(row_color),
fgText=c("orange",
"lightblue",
"orange",
row_color))
}
df <- kableExtra::row_spec(
kable_input=df,
row=which_rows,
background=row_color,
color=setTextContrastColor(row_color));
}
}
# optional column_spec
do_column_spec <- (
length(extra_css) > 0 ||
(length(border_left) > 0 && !FALSE %in% border_left) ||
(length(border_right) > 0 && !FALSE %in% border_right))
if ("kable" %in% return_type &&
!"latex" %in% format &&
TRUE %in% do_column_spec) {
if (length(border_left) == 0) {
border_left <- FALSE;
}
if (length(border_right) == 0) {
border_right <- FALSE;
}
which_columns <- seq_len(ncol(df1) + 1 * (TRUE %in% row.names));
df <- kableExtra::column_spec(
kable_input=df,
column=which_columns,
border_left=border_left,
border_right=border_right,
extra_css=extra_css);
}
df;
}
jmw86069/jamba documentation built on Oct. 9, 2024, 10:52 a.m.
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#' Extend kableExtra colorization of Rmarkdown tables
#'
#' Extend kableExtra colorization of Rmarkdown tables
#'
#' This function extends the `kableExtra` package, and is only
#' available for use if the `kableExtra` package is installed. It is
#' intended to allow specific color assignment of elements in a
#' data.frame, but otherwise uses the `kableExtra` functions to
#' apply those colors.
#'
#' The use case is to provide colorized HTML output for RMarkdown,
#' it has not been tested with other `format` output.
#'
#' The argument `colorSub` accepts:
#'
#' * `character` vector input where
#' names should match column values
#' * `function` that accepts column values and returns a `character`
#' vector of colors of equal length
#' * `list` input where names should match `colnames(df)`, and where
#' each list element should contain either a `character` vector, or
#' `function` as described above.
#'
#' @returns object with class `c("kableExtra", "knitr_kable")` by default
#' when `return_type="kable"`, suitable to render inside an RMarkdown
#' or HTML context. Or returns `data.frame` when `return_type="data.frame"`.
#'
#' @param df `data.frame` input. Note that `kable` input is not supported.
#' @param colorSub one of the following inputs:
#' * `character` vector of R colors, whose names match entries
#' in the `data.frame` which are given these assigned colors
#' * `function` that takes column values as input, and returns
#' a `character` vector with one color per value, using `NA`
#' or `NULL` to indicate `"transparent"`
#' * `list` whose names match `colnames(df)`, where each entry
#' contains either `character` or `function` option as described
#' above. A `character` vector should be named by values expected
#' in each column. A `function` should take column values as input,
#' and return a `character` vector with same length of R colors.
#' @param background_as_tile `logical` default `TRUE`, whether the
#' cell background color will appear as a rounded tile (`TRUE`)
#' or a rectangle (`FALSE`).
#' Either way, the color does not fill the entire whitespace
#' of the table cell, but only around the text itself.
#' @param color_cells `logical` indicating whether to color individual cells,
#' default `TRUE`. This may be `FALSE` when also applying `row_color_by`,
#' so the entire row will be colorized.
#' @param row_color_by `character` vector with one or more `colnames`,
#' indicating how to colorize entire rows of a table.
#' When one column is defined, colors in `colorSub` are used as normal.
#' When multiple columns are defined, values from each column are
#' concatenated using `sep` delimiter. Then resulting values are
#' compared with `colorSub`.
#' @param sep `character` delimiter used to combine values in multiple
#' columns when `row_color_by` is supplied and contains multiple
#' `colnames`. The delimited character strings are compared to
#' `colorSub` to assign colors.
#' @param border_left,border_right,extra_css `character` values optionally
#' passed to `kableExtra::column_spec()` as a convenient way to apply
#' borders for each column (`border_left`, `border_right`) or enable
#' or disable word-wrapping by column. Some helpful examples:
#' * `border_left=FALSE`: disables left border
#' * `border_left="1px solid #DDDDDD"`: light gray 1 pixel left border
#' * `border_right=FALSE`: disables right border
#' * `border_right="1px solid #DDDDDD"`: light gray 1 pixel right border
#' * `extra_css=NULL`: disables word-wrap
#' * `extra_css="whitespace: nowrap;"`: enables text word-wrap
#' * when all options above contain only `FALSE` or `NULL`, then
#' `kableExtra::column_spec()` is not applied.
#' @param format `character` passed to `knitr::kable()`, default `"html"`
#' which is the intended format for most scenarios.
#' It can be set to `NULL` to enable auto-detection of the format.
#' @param format.args `list` of arguments passed to `base::format()`
#' intended mainly for `numeric` columns.
#' @param row.names `logical` indicating whether to include `rownames(df)`.
#' When `row.names=NA` the default is to display rownames if they
#' are not `NULL` and not equal to `1:nrow(df)`.
#' @param align `character` passed to `kableExtra::kable()` to define
#' alignment of each column.
#' @param return_type `character` string indicating the type of data
#' to return.
#' * `return_type="kable"`: (default) returns object with class
#' `"kableExtra", "knitr_kable"` suitable for downstream processing.
#' * `return_type="data.frame"`: returns a `data.frame` whose cells
#' contain HTML markup with corresponding colors defined.
#' @param verbose boolean indicating whether to print verbose output.
#' @param ... additional arguments are passed to `kableExtra::kable()`
#' which allows the usual customizations on the initial call.
#'
#' @returns `data.frame` or class with `"kableExtra"` dependent upon the
#' `return_type` argument. Note that even the `data.frame` returned
#' will have colors encoded into each cell using HTML.
#'
#' @examplesIf all(check_pkg_installed(c("circlize", "kableExtra")))
#' new_colorSub <- list(
#' column_A=nameVector(rainbow(5), LETTERS[1:5]),
#' column_B=nameVector(rev(rainbow(5)), LETTERS[1:5]),
#' column_C=circlize::colorRamp2(
#' colors=getColorRamp("Reds", n=6),
#' breaks=0:5 * 1000))
#' testdf <- data.frame(column_A=LETTERS[1:5],
#' row.names=LETTERS[1:5],
#' column_B=LETTERS[1:5],
#' column_C=1:5 * 1000)
#'
#' # kableExtra output with colored tiles inside table cells
#' kdf1 <- kable_coloring(
#' df=testdf,
#' colorSub=new_colorSub)
#' print(class(kdf1));
#' kdf1;
#'
#' # kableExtra output with colored rows
#' kdf2 <- kable_coloring(
#' row_color_by=3,
#' df=testdf,
#' colorSub=new_colorSub)
#' class(kdf2);
#' kdf2;
#'
#' # data.frame output is a regular data.frame with HTML contents
#' kdf3 <- kable_coloring(
#' return_type="data.frame",
#' df=testdf,
#' colorSub=new_colorSub)
#' kdf3;
#'
#' @family jam color functions
#' @family jam practical functions
#'
#' @export
kable_coloring <- function
(df,
colorSub=NULL,
background_as_tile=TRUE,
color_cells=TRUE,
row_color_by=NULL,
sep="_",
border_left="1px solid #DDDDDD",
border_right=FALSE,
extra_css="white-space: nowrap;",
format="html",
format.args=list(
trim=TRUE,
big.mark=","),
row.names=NA,
align=NULL,
return_type=c("kable",
"data.frame"),
verbose=FALSE,
...)
{
## Purpose is to enhance kableExtra by automating some manual steps
## required to colorize text fields in a data.frame
##
## The input is expected to be a data.frame
if (!check_pkg_installed("kableExtra")) {
stop("kable_coloring() requires the kableExtra package.");
}
return_type <- match.arg(return_type);
# keep a non-kable copy for now
df1 <- df;
if (all(is.na(row.names))) {
if (length(rownames(df)) > 0 &&
!all(rownames(df) == seq_len(nrow(df)))) {
row.names <- TRUE;
} else {
row.names <- FALSE;
}
}
if (length(align) == 0 ||
all(is.na(align)) ||
max(nchar(align), na.rm=TRUE) == 0) {
align <- sapply(seq_len(ncol(df1)), function(i){
if (is.numeric(df[[i]])) {
"r"
} else {
"l"
}
})
} else {
if (max(nchar(align)) == 1) {
align <- rep(align,
length.out=ncol(df));
}
}
if (TRUE %in% color_cells) {
for (i in colnames(df)) {
if (length(colorSub) > 0 && is.list(colorSub)) {
# colorSub as color_list, named by colnames(df)
# if ("color_sub" %in% names(attributes(colorSub))) {}
if (i %in% names(colorSub)) {
if (verbose) {
printDebug("kable_coloring(): ",
"colorizing column:",
i,
" using colorSub[[i]].");
}
icolorSub <- colorSub[[i]];
if (is.function(icolorSub)) {
value_colors <- icolorSub(df[[i]])
} else {
value_colors <- icolorSub[as.character(df[[i]])]
}
column_values <- df[[i]];
if (is.numeric(column_values) && length(format.args) > 0) {
column_values <- do.call(base::format,
c(list(x=column_values),
format.args));
}
df[[i]] <- kableExtra::cell_spec(
x=column_values,
background_as_tile=background_as_tile,
color=setTextContrastColor(
rmNA(value_colors,
naValue="transparent")
),
background=rmNA(value_colors,
naValue="transparent"))
}
} else if (any(as.character(df[[i]]) %in% names(colorSub))) {
# colorSub as named character vector
if (verbose) {
printDebug("kable_coloring(): ",
"colorizing column:",
i);
}
df[[i]] <- kableExtra::cell_spec(df[[i]],
background_as_tile=background_as_tile,
color=setTextContrastColor(
rmNA(colorSub[as.character(df[[i]])],
naValue="transparent")
),
background=rmNA(colorSub[as.character(df[[i]])],
naValue="transparent"))
} else {
if (verbose) {
printDebug("kable_coloring(): ",
"No values to colorize in column:",
i,
fgText=c("orange","red"));
}
}
}
}
## Convert to kable
if (return_type %in% "kable" || length(row_color_by) > 0) {
df <- kableExtra::kable_styling(
kableExtra::kable(x=df,
escape=FALSE,
format=format,
format.args=format.args,
align=align,
row.names=row.names,
...))
}
## Optionally color rows using values in a column
if (length(row_color_by) > 0) {
if (verbose) {
printDebug("kable_coloring(): ",
"row_color_by:",
row_color_by);
}
row_color_by_value <- NULL;
row_colors <- NULL;
if (length(row_color_by) == 1) {
# one column defines the colors used, most common usage
if (length(colorSub) > 0) {
if (is.numeric(row_color_by)) {
row_color_by <- colnames(df1)[row_color_by];
}
row_color_by_value <- df1[[as.character(row_color_by)]]
if (is.list(colorSub)) {
# colorSub is a list named by colnames(df)
icolorSub <- colorSub[[row_color_by]];
if (is.function(icolorSub)) {
row_colors <- icolorSub(row_color_by_value);
} else {
row_colors <- icolorSub[row_color_by_value];
}
} else {
# colorSub is a named character vector, or single color function
if (is.function(colorSub)) {
row_colors <- colorSub(row_color_by_value);
} else {
row_colors <- colorSub[row_color_by_value];
}
}
} else {
# colorSub is empty, do nothing
}
} else {
# two or more columns define the colors used
row_color_by_value <- as.character(
pasteByRow(df1[, row_color_by, drop=FALSE],
sep=sep));
if (length(colorSub) > 0) {
if (is.list(colorSub)) {
# look for attributes "color_sub"
if ("color_sub" %in% names(attributes(colorSub))) {
color_sub <- attr(colorSub, "color_sub");
} else {
color_sub <- unlist(unname(
lapply(colorSub, function(icolorSub){
if (is.function(icolorSub)) {
return(character(0))
}
icolorSub
})))
}
row_colors <- rmNA(naValue="transparent",
color_sub[row_color_by_value])
} else {
# colorSub is a named character vector, or single color function
if (is.function(colorSub)) {
row_colors <- colorSub(row_color_by_value);
} else {
row_colors <- colorSub[row_color_by_value];
}
}
}
}
if (verbose) {
printDebug("kable_coloring(): ",
"row_color_by_value:",
row_color_by_value);
printDebug("kable_coloring(): ",
"row_colors:",
row_colors);
}
row_colors_valid <- unique(rmNA(row_colors));
for (row_color in row_colors_valid) {
which_rows <- which(row_colors %in% row_color);
if (verbose) {
printDebug("kable_coloring(): ",
"colorizing rows:",
which_rows,
closestRcolor(row_color),
fgText=c("orange",
"lightblue",
"orange",
row_color))
}
df <- kableExtra::row_spec(
kable_input=df,
row=which_rows,
background=row_color,
color=setTextContrastColor(row_color));
}
}
# optional column_spec
do_column_spec <- (
length(extra_css) > 0 ||
(length(border_left) > 0 && !FALSE %in% border_left) ||
(length(border_right) > 0 && !FALSE %in% border_right))
if ("kable" %in% return_type &&
!"latex" %in% format &&
TRUE %in% do_column_spec) {
if (length(border_left) == 0) {
border_left <- FALSE;
}
if (length(border_right) == 0) {
border_right <- FALSE;
}
which_columns <- seq_len(ncol(df1) + 1 * (TRUE %in% row.names));
df <- kableExtra::column_spec(
kable_input=df,
column=which_columns,
border_left=border_left,
border_right=border_right,
extra_css=extra_css);
}
df;
}
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