I have a table output in pdf format and I want to customise it to bring in line with a corporate theme. However, I'm new to this area in R and still finding it difficult to find my feet in adding logos.
My original dataset is composed of over 600 rows of data and is sensitive, so I've used a sample dataset to demonstrate. So far, I've got the following code using the grid and gridExtra packages:
library(grid)
library(gridExtra)
Data <- data.frame(Staff = c("Rod","Barry","Cheiny"),
M1 = c(50,40,55),
M2 = c(60,50,55),
M3 = c(55,50,45))
maxrow <- c(35);
npages <- ceiling(nrow(Data)/maxrow);
pdf("Data.pdf", height = 11, width = 10)
idx <- seq(1, maxrow)
grid.table(Data, rows = NULL, theme = ttheme_minimal())
grid.text("data",gp = gpar(fontsize = 12,fontface = "bold",alpha = 0.5),
vjust = -40,
hjust = -0.5)
for (i in 2:npages){
grid.newpage();
if(i*maxrow <= nrow(Data)) {
idx <- seq(1+((i-1)*maxrow), i*maxrow)
}else{
idx <- seq(1+((i-1)*maxrow), nrow(Data))
}
grid.table(Data, rows =NULL, theme = ttheme_minimal())
}
dev.off()
I'm getting a reasonable output at the moment, but I want to add a logo to each of the pages generated.
Anyone know how to add a logo that will repeat across all the pages?
It's easy to add elements with grid.draw(), but the design is up to you
library(grid)
library(gridExtra)
Data <- data.frame(Staff = c("Rod","Barry","Cheiny"),
M1 = c(50,40,55),
M2 = c(60,50,55),
M3 = c(55,50,45))
library(png)
img <- readPNG(system.file("img", "Rlogo.png", package="png"))
footer <- grobTree(rectGrob(y=0,vjust=0,gp=gpar(fill="grey97",col=NA), height=unit(1,"in")),
textGrob(y=unit(0.5,"in"), expression(Corporate^TM~line~(c))),
rasterGrob(img, x=1, hjust=1,y=unit(0.5,"in"),height=unit(1,"in")-unit(2,"mm")))
maxrow <- c(35);
npages <- ceiling(nrow(Data)/maxrow);
pdf("Data.pdf", height = 11, width = 10)
idx <- seq(1, maxrow)
grid.table(Data, rows = NULL, theme = ttheme_minimal())
grid.draw(footer)
grid.text("data",gp = gpar(fontsize = 12,fontface = "bold",alpha = 0.5),
vjust = -40,
hjust = -0.5)
for (i in 2:npages){
grid.newpage();
if(i*maxrow <= nrow(Data)) {
idx <- seq(1+((i-1)*maxrow), i*maxrow)
}else{
idx <- seq(1+((i-1)*maxrow), nrow(Data))
}
grid.table(Data, rows =NULL, theme = ttheme_minimal())
grid.draw(footer)
}
dev.off()
With facet_zoom() from the ggforce package one can create nice zooms to highlight certain regions of a plot. Unfortunately, when zooming in on the y axis the original plot is always on the right side.
Is there a way to place the original plot on the left?
This would feel more intuitive to first look at the main plot and then at the zoomed region. As an example I would like to swap the position of the two facets in this plot:
(No reproducible example added, since I believe this is a question about the existence of a certain functionality.)
I've tweaked the current code for FacetZoom on GitHub to swop the horizontal order from [zoom, original] to [original, zoom]. The changes aren't complicated, but they are scattered throughout draw_panels() function's code, so the full code is rather long.
Result:
# example 1, with split = FALSE, horizontal = TRUE (i.e. default settings)
p1 <- ggplot(mtcars, aes(x = mpg, y = disp, colour = factor(cyl))) +
geom_point() +
theme_bw()
p1 + ggtitle("Original") + facet_zoom(y = disp > 300)
p1 + ggtitle("Modified") + facet_zoom2(y = disp > 300)
# example 2, with split = TRUE
p2 <- ggplot(iris, aes(Petal.Length, Petal.Width, colour = Species)) +
geom_point() +
theme_bw()
p2 + ggtitle("Original") +
facet_zoom(xy = Species == "versicolor", split = TRUE)
p2 + ggtitle("Modified") +
facet_zoom2(xy = Species == "versicolor", split = TRUE)
Code used (I've commented out the original code, where modified code is used, & indicated the packages for functions from other packages):
library(ggplot)
library(ggforce)
library(grid)
# define facet_zoom2 function to use FacetZoom2 instead of FacetZoom
# (everything else is the same as facet_zoom)
facet_zoom2 <- function(x, y, xy, zoom.data, xlim = NULL, ylim = NULL,
split = FALSE, horizontal = TRUE, zoom.size = 2,
show.area = TRUE, shrink = TRUE) {
x <- if (missing(x)) if (missing(xy)) NULL else lazyeval::lazy(xy) else lazyeval::lazy(x)
y <- if (missing(y)) if (missing(xy)) NULL else lazyeval::lazy(xy) else lazyeval::lazy(y)
zoom.data <- if (missing(zoom.data)) NULL else lazyeval::lazy(zoom.data)
if (is.null(x) && is.null(y) && is.null(xlim) && is.null(ylim)) {
stop("Either x- or y-zoom must be given", call. = FALSE)
}
if (!is.null(xlim)) x <- NULL
if (!is.null(ylim)) y <- NULL
ggproto(NULL, FacetZoom2,
shrink = shrink,
params = list(
x = x, y = y, xlim = xlim, ylim = ylim, split = split, zoom.data = zoom.data,
zoom.size = zoom.size, show.area = show.area,
horizontal = horizontal
)
)
}
# define FacetZoom as a ggproto object that inherits from FacetZoom,
# with a modified draw_panels function. the compute_layout function references
# the version currently on GH, which is slightly different from the CRAN
# package version.
FacetZoom2 <- ggproto(
"FacetZoom2",
ggforce::FacetZoom,
compute_layout = function(data, params) {
layout <- rbind( # has both x & y dimension
data.frame(name = 'orig', SCALE_X = 1L, SCALE_Y = 1L),
data.frame(name = 'x', SCALE_X = 2L, SCALE_Y = 1L),
data.frame(name = 'y', SCALE_X = 1L, SCALE_Y = 2L),
data.frame(name = 'full', SCALE_X = 2L, SCALE_Y = 2L),
data.frame(name = 'orig_true', SCALE_X = 1L, SCALE_Y = 1L),
data.frame(name = 'zoom_true', SCALE_X = 1L, SCALE_Y = 1L)
)
if (is.null(params$y) && is.null(params$ylim)) { # no y dimension
layout <- layout[c(1,2, 5:6),]
} else if (is.null(params$x) && is.null(params$xlim)) { # no x dimension
layout <- layout[c(1,3, 5:6),]
}
layout$PANEL <- seq_len(nrow(layout))
layout
},
draw_panels = function(panels, layout, x_scales, y_scales, ranges, coord,
data, theme, params) {
if (is.null(params$x) && is.null(params$xlim)) {
params$horizontal <- TRUE
} else if (is.null(params$y) && is.null(params$ylim)) {
params$horizontal <- FALSE
}
if (is.null(theme[['zoom']])) {
theme$zoom <- theme$strip.background
}
if (is.null(theme$zoom.x)) {
theme$zoom.x <- theme$zoom
}
if (is.null(theme$zoom.y)) {
theme$zoom.y <- theme$zoom
}
axes <- render_axes(ranges, ranges, coord, theme, FALSE)
panelGrobs <- ggforce:::create_panels(panels, axes$x, axes$y)
panelGrobs <- panelGrobs[seq_len(length(panelGrobs) - 2)]
if ('full' %in% layout$name && !params$split) {
panelGrobs <- panelGrobs[c(1, 4)]
}
# changed coordinates in indicator / lines to zoom from
# the opposite horizontal direction
if ('y' %in% layout$name) {
if (!inherits(theme$zoom.y, 'element_blank')) {
zoom_prop <- scales::rescale(
y_scales[[2]]$dimension(ggforce:::expansion(y_scales[[2]])),
from = y_scales[[1]]$dimension(ggforce:::expansion(y_scales[[1]])))
indicator <- polygonGrob(
x = c(0, 0, 1, 1), # was x = c(1, 1, 0, 0),
y = c(zoom_prop, 1, 0),
gp = gpar(col = NA, fill = alpha(theme$zoom.y$fill, 0.5)))
lines <- segmentsGrob(
x0 = c(1, 1), x1 = c(0, 0), # was x0 = c(0, 0), x1 = c(1, 1)
y0 = c(0, 1), y1 = zoom_prop,
gp = gpar(col = theme$zoom.y$colour,
lty = theme$zoom.y$linetype,
lwd = theme$zoom.y$size,
lineend = 'round'))
indicator_h <- grobTree(indicator, lines)
} else {
indicator_h <- zeroGrob()
}
}
if ('x' %in% layout$name) {
if (!inherits(theme$zoom.x, 'element_blank')) {
zoom_prop <- scales::rescale(x_scales[[2]]$dimension(ggforce:::expansion(x_scales[[2]])),
from = x_scales[[1]]$dimension(ggforce:::expansion(x_scales[[1]])))
indicator <- polygonGrob(c(zoom_prop, 1, 0), c(1, 1, 0, 0),
gp = gpar(col = NA, fill = alpha(theme$zoom.x$fill, 0.5)))
lines <- segmentsGrob(x0 = c(0, 1), y0 = c(0, 0), x1 = zoom_prop, y1 = c(1, 1),
gp = gpar(col = theme$zoom.x$colour,
lty = theme$zoom.x$linetype,
lwd = theme$zoom.x$size,
lineend = 'round'))
indicator_v <- grobTree(indicator, lines)
} else {
indicator_v <- zeroGrob()
}
}
if ('full' %in% layout$name && params$split) {
space.x <- theme$panel.spacing.x
if (is.null(space.x)) space.x <- theme$panel.spacing
space.x <- unit(5 * as.numeric(convertUnit(space.x, 'cm')), 'cm')
space.y <- theme$panel.spacing.y
if (is.null(space.y)) space.y <- theme$panel.spacing
space.y <- unit(5 * as.numeric(convertUnit(space.y, 'cm')), 'cm')
# change horizontal order of panels from [zoom, original] to [original, zoom]
# final <- gtable::gtable_add_cols(panelGrobs[[3]], space.x)
# final <- cbind(final, panelGrobs[[1]], size = 'first')
# final_tmp <- gtable::gtable_add_cols(panelGrobs[[4]], space.x)
# final_tmp <- cbind(final_tmp, panelGrobs[[2]], size = 'first')
final <- gtable::gtable_add_cols(panelGrobs[[1]], space.x)
final <- cbind(final, panelGrobs[[3]], size = 'first')
final_tmp <- gtable::gtable_add_cols(panelGrobs[[2]], space.x)
final_tmp <- cbind(final_tmp, panelGrobs[[4]], size = 'first')
final <- gtable::gtable_add_rows(final, space.y)
final <- rbind(final, final_tmp, size = 'first')
final <- gtable::gtable_add_grob(final, list(indicator_h, indicator_h),
c(2, 6), 3, c(2, 6), 5,
z = -Inf, name = "zoom-indicator")
final <- gtable::gtable_add_grob(final, list(indicator_v, indicator_v),
3, c(2, 6), 5,
z = -Inf, name = "zoom-indicator")
heights <- unit.c(
unit(max_height(list(axes$x[[1]]$top, axes$x[[3]]$top)), 'cm'),
unit(1, 'null'),
unit(max_height(list(axes$x[[1]]$bottom, axes$x[[3]]$bottom)), 'cm'),
space.y,
unit(max_height(list(axes$x[[2]]$top, axes$x[[4]]$top)), 'cm'),
unit(params$zoom.size, 'null'),
unit(max_height(list(axes$x[[2]]$bottom, axes$x[[4]]$bottom)), 'cm')
)
# swop panel width specifications according to the new horizontal order
widths <- unit.c(
# unit(max_width(list(axes$y[[3]]$left, axes$y[[4]]$left)), 'cm'),
# unit(params$zoom.size, 'null'),
# unit(max_height(list(axes$y[[3]]$right, axes$y[[4]]$right)), 'cm'),
# space.x,
# unit(max_width(list(axes$y[[1]]$left, axes$y[[2]]$left)), 'cm'),
# unit(1, 'null'),
# unit(max_height(list(axes$y[[1]]$right, axes$y[[2]]$right)), 'cm')
unit(max_width(list(axes$y[[1]]$left, axes$y[[2]]$left)), 'cm'),
unit(1, 'null'),
unit(max_height(list(axes$y[[1]]$right, axes$y[[2]]$right)), 'cm'),
space.x,
unit(max_width(list(axes$y[[3]]$left, axes$y[[4]]$left)), 'cm'),
unit(params$zoom.size, 'null'),
unit(max_height(list(axes$y[[3]]$right, axes$y[[4]]$right)), 'cm')
)
final$heights <- heights
final$widths <- widths
} else {
if (params$horizontal) {
space <- theme$panel.spacing.x
if (is.null(space)) space <- theme$panel.spacing
space <- unit(5 * as.numeric(convertUnit(space, 'cm')), 'cm')
heights <- unit.c(
unit(max_height(list(axes$x[[1]]$top, axes$x[[2]]$top)), 'cm'),
unit(1, 'null'),
unit(max_height(list(axes$x[[1]]$bottom, axes$x[[2]]$bottom)), 'cm')
)
# change horizontal order of panels from [zoom, original] to [original, zoom]
# first <- gtable::gtable_add_cols(panelGrobs[[2]], space)
# first <- cbind(final, panelGrobs[[1]], size = 'first')
final <- gtable::gtable_add_cols(panelGrobs[[1]], space)
final <- cbind(final, panelGrobs[[2]], size = "first")
final$heights <- heights
# swop panel width specifications according to the new horizontal order
# unit(c(params$zoom.size, 1), 'null')
final$widths[panel_cols(final)$l] <- unit(c(1, params$zoom.size), 'null')
final <- gtable::gtable_add_grob(final, indicator_h, 2, 3, 2, 5,
z = -Inf, name = "zoom-indicator")
} else {
space <- theme$panel.spacing.y
if (is.null(space)) space <- theme$panel.spacing
space <- unit(5 * as.numeric(convertUnit(space, 'cm')), 'cm')
widths <- unit.c(
unit(max_width(list(axes$y[[1]]$left, axes$y[[2]]$left)), 'cm'),
unit(1, 'null'),
unit(max_height(list(axes$y[[1]]$right, axes$y[[2]]$right)), 'cm')
)
final <- gtable::gtable_add_rows(panelGrobs[[1]], space)
final <- rbind(final, panelGrobs[[2]], size = 'first')
final$widths <- widths
final$heights[panel_rows(final)$t] <- unit(c(1, params$zoom.size), 'null')
final <- gtable::gtable_add_grob(final, indicator_v, 3, 2, 5,
z = -Inf, name = "zoom-indicator")
}
}
final
}
)
Note: create_panels and expansion are un-exported functions from the ggforce package, so I referenced them with triple colons. This isn't robust for writing packages, but should suffice as a temporary workaround.
Update 30 Oct 2019: A suggestion for those seeing errors like Invalid 'type' (list) of argument after trying to use this solution as-is. The issue is likely due to updates made to the ggforcepackage since this solution was developed. To get the code in this solution working again, install the version of ggforce that was available when the solution was developed. This can be done with the devtools package pointing to the 4008a2e commit:
devtools::install_github("thomasp85/ggforce", ref = '4008a2e')
I'm trying to generate heatmaps by using cellrangerRkit package. The function within this package refers to pheatmap function featured in pheatmap library as seen below:
gbm_pheatmap
function (gbm, genes_to_plot, cells_to_plot, n_genes = 5, colour = NULL,
limits = c(-3, 3))
{
if (!is.list(genes_to_plot)) {
cat("Plotting one gene set instead of multiple cluster-specific gene sets\n")
gene_indices <- sapply(genes_to_plot, function(x) get_gene_index(gbm,
x))
gene_annotation <- NULL
}
else {
if ("significant" %in% names(genes_to_plot[[1]])) {
gene_indices <- unlist(lapply(genes_to_plot, function(x) with(x,
head(ix[significant], n_genes))))
gene_grouping <- unlist(lapply(names(genes_to_plot),
function(nm) rep(nm, with(genes_to_plot[[nm]],
length(head(ix[significant], n_genes))))))
}
else {
gene_indices <- unlist(lapply(genes_to_plot, function(x) x$ix[1:n_genes]))
gene_grouping <- rep(names(genes_to_plot), each = n_genes)
}
gene_annotation <- data.frame(ClusterID = as.factor(gene_grouping))
}
cell_indices <- unlist(lapply(cells_to_plot, function(x) x$ix))
value <- t(scale(t(as.matrix(exprs(gbm))[gene_indices, cell_indices])))
value[value < limits[1]] <- limits[1]
value[value > limits[2]] <- limits[2]
rownames(value) <- make.unique(fData(gbm)$symbol[gene_indices])
cell_grouping <- unlist(lapply(1:length(cells_to_plot), function(x) {
rep(names(cells_to_plot)[x], length(cells_to_plot[[x]]$barcode))
}))
cell_annotation <- data.frame(ClusterID = as.factor(cell_grouping))
rownames(cell_annotation) <- colnames(value)
if (!is.null(gene_annotation)) {
rownames(gene_annotation) <- rownames(value)
}
if (is.null(colour)) {
anno_colors <- NULL
}
else {
names(colour) <- names(cells_to_plot)
anno_colors <- list(ClusterID = colour)
}
pheatmap(value, cluster_rows = FALSE, cluster_cols = FALSE,
show_colnames = FALSE, annotation_row = gene_annotation,
annotation_col = cell_annotation, annotation_names_row = FALSE,
annotation_names_col = FALSE, annotation_colors = anno_colors)
}
<bytecode: 0x00000000507b7970>
<environment: namespace:cellrangerRkit>
My problem is that, when I plot my heatmap, the annotation on the right side of the plot is overlapping due to large font size (see below)
The wrapper function gbm_heatmap doesn't have a fontsize option, preventing me from simply passing an argument when calling it. How I can change the plotting behavior within this wrapper?
Appreciate all the input, thanks!
I want to export my dataframe to a pdf file. Dataframe is pretty large, so it is causing problems while exporting. I used gridExtra package as specified here writing data frame to pdf table but it did not work for my dataframe as it contains a lot of data.
Any ideas how it can be achieved?
Code:
library(gridExtra)
df <- data.frame(replicate(10,sample(0:1,1000,rep=TRUE)))
pdf(file = "df2.pdf")
grid.table(df)
dev.off()
#Baqir, you can try solution given on this link:
https://thusithamabotuwana.wordpress.com/2016/01/02/creating-pdf-documents-with-rrstudio/
It will be like this:
library(grid)
library(gridExtra)
df <- data.frame(replicate(10,sample(0:1,1000,rep=TRUE)))
dim(df)
maxrow = 35
npages = ceiling(nrow(df)/maxrow)
pdf("test.pdf", height = 11, width = 8.5)
idx = seq(1, maxrow)
grid.table(df[idx,],rows = NULL)
for(i in 2:npages){
grid.newpage();
if(i*maxrow <= nrow(df)){
idx = seq(1+((i-1)*maxrow), i * maxrow)
}
else{
idx = seq(1+((i-1)*maxrow), nrow(df))
}
grid.table(df[idx, ],rows = NULL)
}
dev.off()
Hope this works!
#Pryore, I found some part of the solution from the link:
link
Here is the code for header and footer.
Hope this works!
makeHeader <- function(headerText= "your header", size= 1, color= grey(.5))
{
require(grid)
pushViewport(viewport())
grid.text(label= headerText,
x = unit(1,"npc") - unit(110, "mm"),
y = unit(270.8, "mm"),
gp=gpar(cex= size, col=color))
popViewport()
}
makeFootnote <- function(footnoteText= "your footnote",
size= 1, color= grey(.5))
{
require(grid)
pushViewport(viewport())
grid.text(label= footnoteText ,
x = unit(1,"npc") - unit(27, "mm"),
y = unit(3, "mm"),
gp=gpar(cex= size, col=color))
popViewport()
}
library(grid)
library(gridExtra)
df <- data.frame(replicate(10,sample(0:1,1000,rep=TRUE)))
dim(df)
maxrow = 35
npages = ceiling(nrow(df)/maxrow)
pdf("trial.pdf", height = 11, width = 8.5)
idx = seq(1, maxrow)
grid.table(df[idx,],rows = NULL)
for(i in 1:npages){
grid.newpage();
makeFootnote()
makeHeader()
if(i*maxrow <= nrow(df)){
idx = seq(1+((i-1)*maxrow), i * maxrow)
}
else{
idx = seq(1+((i-1)*maxrow), nrow(df))
}
grid.table(df[idx, ],rows = NULL)
}
dev.off()
I'm trying to output some of my code results in knitr. Now the strange thing is, the code generates the error in the title. But running round_any() seperately and outputting it in knitr is fine.
knitr code
```{r, echo = FALSE, message=FALSE, warning=FALSE}
source("BooliQuery.R")
BooliQuery()
```
My code
library(digest)
library(stringi)
library(jsonlite)
library(plyr)
BooliQuery <- function(area = "stockholm", type="lägenhet", sincesold = "", FUN = "", limit = 250, offset = 0, mode = 1) {
#raw data fetch + adjust.
lOriginal <- GETAPI(area, type, sincesold, FUN, limit, offset)
lOriginal$AreaSize <- round_any(lOriginal$livingArea, 10, floor)
lOriginal$PriceDiff <- lOriginal$soldPrice - lOriginal$listPrice
#Create frame overview
Overview.Return <- Frame.Overview(lOriginal)
#Mode - return selector
ifelse( mode == 1, return (Overview.Return), return (lOriginal) )
}
Frame.Overview <- function(lOriginal) {
#Aggregate mean
listPrice <- aggregate(lOriginal, list(lOriginal$AreaSize), FUN = mean, na.rm = TRUE)
colnames(listPrice)[1] <- "SegGroup"
listPrice <- listPrice[, c("SegGroup", "listPrice", "soldPrice", "PriceDiff", "rent", "livingArea", "constructionYear") ]
#Perform Rounding
listPrice[, c(2:5)] <- round(listPrice[,c(2:5)], digits = 0)
listPrice[, 6] <- round(listPrice[, 6], digits = 1)
listPrice[, 7] <- signif(listPrice[,7], digits = 4)
return(listPrice)
}
GETAPI <- function(area = "stockholm", type="lägenhet", sincesold = "", FUN = "", limit = 250, offset = 0) {
#ID Info
key <- "PRIVATE KEY"
caller.ID <- "USERNAME"
#//
unix.timestamp <- as.integer( as.POSIXct(Sys.time()) )
random.string <- stri_rand_strings( n = 1, length = 16)
#Sha1-Hash: CallerID + time + key + unique, 40-char hexadecimal
hash.string <- paste0(caller.ID, unix.timestamp, key, random.string)
hash.sha1 <- digest(hash.string,"sha1",serialize=FALSE)
#Create URL
api.string <- "https://api.booli.se/sold?q="
url.string <- paste0(api.string, area, "&objectType=" , type , "&minSoldDate=", sincesold, FUN, "&limit=", limit, "&offset=", offset,"&callerId=", caller.ID, "&time=" ,
unix.timestamp, "&unique=", random.string, "&hash=", hash.sha1)
#Parse JSON
parsed.JSON <- fromJSON(txt = url.string)
return(parsed.JSON$sold)
}
Running the code seperately in console is fine. So what could be wrong?