KableExtra html table not collapsing rows - html

I have a simple Table that I want to visualize in an html format using kableExtra. This table has a few repeated cells in the first column and I would like to collapse these cells into one. Only problem is that the package isn't letting me do that. How can I solve this?
This is my data:
df <- data.frame( Vegitation = c("Tree", "Tree", "Tree" , "Fruit", "Fruit", "Water"),
Non_sense_var1 = c(17,14,1,20,21,0),
Non_sense_var2 = c(15,1,11,2,2.1,60),
Non_sense_var3 = c(4,6,14,2,7,7)
)
And this is the code for my table:
header_line <- c("Vegitation", "Value 1", "Value 2", "Value 3")
kbl(df, escape = F, align = 'lcccc')%>%
add_header_above( header_line, bold = T, line = F, font_size = 11) %>%
kable_styling(full_width = T, font_size = 10, html_font = 'arial') %>%
kable_classic() %>%
column_spec(1, width = "2.2cm", bold = TRUE ) %>%
column_spec(2, width = "2.2cm") %>%
column_spec(c(3:4), width = "2.2cm", color = '#FF7F0E') %>%
collapse_rows(1, valign = "top")
And when I try to run this code, this is what I get:
EDIT: Currently (the date being Sept. 27 2022), KableExtra has issues when collapsing rows in similar scenarios as to mentioned here. There is no official production fix in yet. You can try the fix via github update but what that did for me was mess up other formatting of my table. You can also try another package for your use case. As of now, those seem like the possible available options.

Given this issue seems to have been persistent with the kbl (https://github.com/haozhu233/kableExtra/issues/624), you may consider another package such as reactable, huxatable, or gt
a couple of examples:
df <- data.frame( Vegitation = c("Tree", "Tree", "Tree" , "Fruit", "Fruit", "Water"),
Non_sense_var1 = c(17,14,1,20,21,0),
Non_sense_var2 = c(15,1,11,2,2.1,60),
Non_sense_var3 = c(4,6,14,2,7,7)
)
header_line <- c("Vegitation", "Value 1", "Value 2", "Value 3")
library(reactable)
reactable(df,
columns = list(
Vegitation = colDef(
style = JS("function(rowInfo, column, state) {
const firstSorted = state.sorted[0]
// Merge cells if unsorted or sorting by school
if (!firstSorted || firstSorted.id === 'Vegitation') {
const prevRow = state.pageRows[rowInfo.viewIndex - 1]
if (prevRow && rowInfo.values['Vegitation'] === prevRow['Vegitation']) {
return { visibility: 'hidden' }
}
}
}"))))
library(gt)
df <- df %>%
group_by(Vegitation)
gt(df)

Related

DT table in Shiny (overriding custom css) - How to color the whole row based on a value in a specific column?

I am trying to color the top two rows differently from the rest of the table as it contains control samples. The table is made using DT for Shiny app.
Desired output:
Actual output:
The code:
output$table <- renderDataTable({
dt <- dt %>% datatable(rownames=FALSE, class="table table-hover row-border", extensions = c( 'FixedHeader'),
options = list( scrollX = TRUE, pageLength = -1,dom = 'Btpl', ordering = TRUE,
dom="ft",
lengthMenu = list(c(10,25,-1),
c(10,25,"All")),
columnDefs = list(list(visible=FALSE, targets=c(7,8)))
)) %>%
formatStyle('Sample',
fontWeight ='bold',
backgroundColor = styleEqual(c("Positive control", "Negative control"),
c("#fcf4d9", "#fcf4d9")))
})
I have tried adding target = "row" argument but it doesn't work. I also tried to use styleRow() instead of styleEqual() but this resulted in error "coercion of NA values".
Update:
The default bakcground colors are specified in tags$style that is why it doesn't work using format style:
tags$style(HTML(sprintf('table.dataTable tbody tr {background-color: %1$s !important; color: %2$s !important;}',
table_col,font_col_dark)))
I am not that familiar with this expression, but is it possible to specify the bakcground color for controls in tags instead?
Adding target = 'row' should be the solution:
Code:
# Data
dt <- tibble(Well = 1:5, Sample = c("Positive control", "Negative control", "Sample 1", "Sample 2", "Sample 3"), Result = 10:14)
# Table
dt %>% datatable(rownames=FALSE, class="table table-hover row-border", extensions = c( 'FixedHeader'),
options = list( scrollX = TRUE, pageLength = -1,dom = 'Btpl', ordering = TRUE,
dom="ft",
lengthMenu = list(c(10,25,-1),
c(10,25,"All")),
columnDefs = list(list(visible=FALSE, targets=c(7,8)))
)) %>%
formatStyle('Sample',
fontWeight ='bold',
target = 'row',
backgroundColor = styleEqual(c("Positive control", "Negative control"),
c("#fcf4d9", "#fcf4d9")))
Update:
You might control the background color by using some helper vectors instead:
# Data
dt <- tibble(Well = 1:5, Sample = c("Positive control", "Negative control", "Sample 1", "Sample 2", "Sample 3"), Result = 10:14)
# Helper
id_helper <- unique(dt$Sample)
color_helper <- ifelse(id_helper %in% c("Positive control", "Negative control"), '#fcf4d9', 'blue')
# Table
dt %>% datatable(rownames=FALSE, class="table table-hover row-border", extensions = c( 'FixedHeader'),
options = list( scrollX = TRUE, pageLength = -1,dom = 'Btpl', ordering = TRUE,
dom="ft",
lengthMenu = list(c(10,25,-1),
c(10,25,"All")),
columnDefs = list(list(visible=FALSE, targets=c(7,8)))
)) %>%
formatStyle('Sample',
fontWeight ='bold',
target = 'row',
backgroundColor = styleEqual(id_helper,
color_helper))

Several lines with different style in Caption in both html and docx - flextable

I need to show data caption, computer name and period in the header of table.
I have also requirements: zebra theme, merging cells if needed. That's why I chose flextable.
Here is my code:
library(officer) # border settings library
library(flextable) # drawing tables library
library(dplyr)
Caption <- "<b><big>Computer01.domain.com</big></b><br>Network Interface<br>Gbit Total/sec<br><small>2021-05-14 18:04 to 2021-05-25 13:29</small>"
bold_border <- fp_border(color="gray", width =2)
std_border <- fp_border(color="gray")
stub <- "2021-05-14 01:40 to 2021-05-17 08:26"
table_data <- data.frame (
Instance = c("Intel[R] Ethernet 10G",
"Intel[R] Ethernet Converged Network Adapter _1",
"Intel[R] Ethernet Converged Network Adapter _2",
"Intel[R] Ethernet 10G",
"Intel[R] Gigabit"),
Max = c(2.45, 2.41, 2.29, 2.17, 0),
Avg = c(0.15, 0.15, 0.15, 0.17, 0)
)
table <- table_data %>% flextable() %>%
set_caption(caption = Caption , html_escape = F) %>%
bg(bg = "#579FAD", part = "header") %>%
color(color = "white", part = "header") %>%
theme_zebra(
odd_header = "#579FAD",
odd_body = "#E0EFF4",
even_header = "transparent",
even_body = "transparent"
) %>%
set_table_properties(width = 1, layout = "autofit") %>%
hline(part="all", border = std_border ) %>%
vline(part="all", border = std_border ) %>%
border_outer( border = bold_border, part = "all" ) %>%
fix_border_issues() %>%
set_header_labels(
values = list(Instance = InstanceName ) ) %>%
flextable::font (part = "all" , fontname = "Calibri")
save_as_docx( table, path = file.path("c:\\temp", "test01.docx") )
save_as_html (table, path = file.path("c:\\temp", "test01.html"))
Here is what I got in html which is okay for me:
But in docx format my header style is not applied:
How can I create header like I did for html that can be saved to both html and docx?
If I have to create separate tables - one for html, other for docx - it's not so good but acceptable options. That case my question how to create header I made in html but for docx format?

R: saving multiple html widgets together

I am using the R programming language. I am interested in learning how to save several "html widgets" together. I have been able to manually create different types of html widgets:
#widget 1
library(htmlwidgets)
library(leaflet)
library(RColorBrewer)
# create map data
map_data <- data.frame(
"Lati" = c(43.6426, 43.6424, 43.6544, 43.6452, 43.6629), "Longi" = c(-79.3871, -79.3860, -79.3807, -79.3806, -79.3957),
"Job" = c("Economist", "Economist", "Teacher", "Teacher", "Lawyer"),
"First_Name" = c("John", "James", "Jack", "Jason", "Jim"),
"Last_Name" = c("Smith", "Charles", "Henry", "David", "Robert"),
"vehicle" = c("car", "van", "car", "none", "car")
)
kingdom <- c("Economist", "Lawyer", "Teacher")
my_palette <- brewer.pal(3, "Paired")
factpal <- colorFactor(my_palette, levels = kingdom)
groups <- unique(map_data$Job)
# finalize map
map <- leaflet(map_data) %>%
addTiles(group = "OpenStreetMap") %>%
addCircleMarkers(~Longi, ~Lati, popup = ~Job,
radius = 10, weight = 2, opacity = 1, color = ~factpal(Job),
fill = TRUE, fillOpacity = 1, group = ~Job
)
widget_1 = map %>%
addLayersControl(overlayGroups = groups, options = layersControlOptions(collapsed = FALSE)) %>%
addTiles() %>%
addMarkers(lng = ~Longi,
lat = ~Lati,
popup = ~paste("Job", Job, "<br>",
"First_Name:", First_Name, "<br>",
"Last_Name:", Last_Name, "<br>", "vehicle:", vehicle, "<br>"))
widget 2:
##### widget 2
library(plotly)
library(ggplot2)
p_plot <- data.frame(frequency = c(rnorm(31, 1), rnorm(31)),
is_consumed = factor(round(runif(62))))
p2 <- p_plot %>%
ggplot(aes(frequency, fill = is_consumed)) +
geom_density(alpha = 0.5)
widget_2 = ggplotly(p2)
widget 3:
#####widget_3
today <- Sys.Date()
tm <- seq(0, 600, by = 10)
x <- today - tm
y <- rnorm(length(x))
widget_3 <- plot_ly(x = ~x, y = ~y, mode = 'lines', text = paste(tm, "days from today"))
widget 4:
####widget_4
library(igraph)
library(dplyr)
library(visNetwork)
Data_I_Have <- data.frame(
"Node_A" = c("John", "John", "John", "Peter", "Peter", "Peter", "Tim", "Kevin", "Adam", "Adam", "Xavier"),
"Node_B" = c("Claude", "Peter", "Tim", "Tim", "Claude", "Henry", "Kevin", "Claude", "Tim", "Henry", "Claude")
)
graph_file <- data.frame(Data_I_Have$Node_A, Data_I_Have$Node_B)
colnames(graph_file) <- c("Data_I_Have$Node_A", "Data_I_Have$Node_B")
graph <- graph.data.frame(graph_file, directed=F)
graph <- simplify(graph)
nodes <- data.frame(id = V(graph)$name, title = V(graph)$name)
nodes <- nodes[order(nodes$id, decreasing = F),]
edges <- get.data.frame(graph, what="edges")[1:2]
widget_4 = visNetwork(nodes, edges) %>% visIgraphLayout(layout = "layout_with_fr") %>%
visOptions(highlightNearest = TRUE, nodesIdSelection = TRUE)
From here, I found another stackoverflow post where a similar question was asked: Using R and plot.ly, how to save multiples htmlwidgets to my html?
In this post, it explains how to save several html widgets together - the person who answered the question wrote a function to do so:
library(htmltools)
save_tags <- function (tags, file, selfcontained = F, libdir = "./lib")
{
if (is.null(libdir)) {
libdir <- paste(tools::file_path_sans_ext(basename(file)),
"_files", sep = "")
}
htmltools::save_html(tags, file = file, libdir = libdir)
if (selfcontained) {
if (!htmlwidgets:::pandoc_available()) {
stop("Saving a widget with selfcontained = TRUE requires pandoc. For details see:\n",
"https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md")
}
htmlwidgets:::pandoc_self_contained_html(file, file)
unlink(libdir, recursive = TRUE)
}
return(htmltools::tags$iframe(src= file, height = "400px", width = "100%", style="border:0;"))
}
I tried using this function to save the 4 widgets together:
save_tags(widget_1, widget_2, widget_3, widget_4)
But doing so, I got the following error:
Error in dirname(file) : a character vector argument expected
Is there a straightforward and simple way for saving multiple html widgets together?
Thanks
NOTE: I know that you can use the combineWidgets() function in R:
library(manipulateWidget)
combineWidgets(widget_1, widget_2, widget_3, widget_4)
However, I am working with a computer that has no internet access or USB ports. This computer has a pre-installed copy of R with limited libraries (it has all the libraries used throughout my question except "manipulateWidget"). I am looking for the simplest way to save multiple html widgets together (e.g. is this possible in base R)?
Thanks
If format doesn't matter too much, you can merge the widgets using tagList and save them directly:
htmltools::save_html(tagList(widget_1, widget_2, widget_3, widget_4), file = "C://Users//Me//Desktop//widgets.html")
(It goes without saying that you will need to edit the filepath!)
If you want to control the layout of the widgets, you can wrap each in a div, and then style those:
doc <- htmltools::tagList(
div(widget_1, style = "float:left;width:50%;"),
div(widget_2,style = "float:left;width:50%;"),
div(widget_3, style = "float:left;width:50%;"),
div(widget_4, style = "float:left;width:50%;")
)
htmltools::save_html(html = doc, file = "C://Users//Me//Desktop//widgets.html")

Embedding flextable in outlook with rdcomclient

I am facing the following issue: I created a beautiful flextable from a dataframe in R, which I would like to send via email. I use htmltools_value to get the HTML code of the flextable. Now I am able to embed this as htmlbody in my email which works in a sense that I succesfully send the email. However, the email is losing all the colors and borders with rest of the formatting still as defined in the flextable. Anyone faced similar issues or has an idea what could be the problem?
require(flextable)
require(RDCOMClient)
header_col2 <- c("","","", "", "2nd header", "2nd header","More headers", "More headers", "More headers", "More headers")
dfTest <- mtcars[c(1:6),c(1:10)]
ft <- flextable(dfTest)
ft <- add_header_row(ft,values = header_col2,top = T,colwidths = c(rep(1,10))) ft <- merge_h(ft, part = "header")
ft <-bold(ft, bold=T, part="header")
ft <-theme_zebra(ft,odd_header = 'red', even_header = 'grey', odd_body = 'lightblue', even_body = "white")
ft <- color(ft, color = "white", part = "header")
ft <- bold(ft, bold = TRUE, part = "header")
ft <- fontsize(ft, size = 11, part = "header")
std_border = fp_border(color="white", width = 1.5)
big_border = fp_border(color="gray", width = 1)
ft <- border_outer(ft, part="all", border = big_border )
ft <- border_inner_v(ft, part="header", border = std_border )
body <- htmltools_value(ft)
# or body <- format(ft, type = "html")
OutApp <- COMCreate("Outlook.Application")
outMail = OutApp$CreateItem(0)
outMail[["To"]] = "test#test.com"
outMail[["subject"]] = "TEST"
outMail[["HTMLbody"]] = body
outMail$Send()

labels in leaflet r with HTML tags

All good souls, help needed. I am creating a leaflet map and cannot resolve a strange issue with labels. I created labels with few variables and the labels render ok if the first variable is numeric, but they fail if the first is a string - any idea what's the issue?
Let's start with a dummy spdf:
library(htmltools)
library(sp)
library(leaflet)
df <- new("SpatialPointsDataFrame", data = structure(list(PMID = c(184397, 184397), SPACEID = c("184397_1", "184397_2")), .Names = c("PMID", "SPACEID"), row.names = 1:2, class = "data.frame"), coords.nrs = numeric(0), coords = structure(c(-0.14463936, -0.14468822, 51.50726534, 51.50730171), .Dim = c(2L, 2L), .Dimnames = list(c("1", "2"), c("x", "y"))), bbox = structure(c(-0.14468822, 51.50726534, -0.14463936, 51.50730171), .Dim = c(2L, 2L), .Dimnames = list(c("x", "y"), c("min", "max"))), proj4string = new("CRS", projargs = "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"))
now we (m)apply a simple HTML line (the original used the df rows but it is not needed and can be simplified to
df#data$HT<-mapply(function(x,y){htmltools::HTML(sprintf("<h2>%s</h2> %s",x,y))},1,"L", SIMPLIFY = F)
and this one will work fine. But if the order is reversed - instead of (1,"L") we change to ("L",1) - it fails:
df#data$HT<-mapply(function(x,y){htmltools::HTML(sprintf("<h2>%s</h2> %s",x,y))},"L",1, SIMPLIFY = F)
in the first case the map contains correct labels and in the other one it produces empty label
leaflet() %>%
addTiles() %>%
addMarkers(data = df, label = ~ HT)
if I use label = ~as.character(HT) it shall produce a verbatim HTML tag, but not the label. What's wrong with it?
After playing around the code, I found that replacing mapply() with map2() in the purrr package does the trick here. I am not totally sure why this is the case. Both Slav and I confirmed that this solution is working on our machines.
library(sp)
library(leaflet)
library(htmltools)
library(purrr)
df#data$HT1 <- map2(1, "L", ~htmltools::HTML(sprintf("<h2>%s</h2> %s",.x,.y)))
df#data$HT2 <- map2("L", 1, ~htmltools::HTML(sprintf("<h2>%s</h2> %s",.x,.y)))
leaflet()%>%
addProviderTiles("OpenStreetMap.Mapnik") %>%
addLabelOnlyMarkers(data = df, label = ~HT2,
labelOptions = labelOptions(noHide = TRUE, direction = 'center',
textOnly = FALSE, textsize = "15px"))