I want to use xtable layouts in my powerpoint presentations and I need a way to directly convert a data.frame into a picture or plot of an xtable such as the ones displayed here.
The ideal solution would give me a ggplot object as I have the most flexibility from there, but I can work with another output as long as I can see a xtable in a pic (raster or vector) or plot window.
Using ggplot2 and grid.extra we can achieve decently looking tables:
library(ggplot2)
library(gridExtra)
ggplot() + annotation_custom(tableGrob(head(iris))) + theme_void()
tableGrob has a theme parameter that allows enough flexibility to reproduce something close to xtable. see this vignette.
Here's a convenient function to do a bit more, you'll need packages grid and gtable :
table_plot <- function(x,
theme_fun= gridExtra::ttheme_minimal,
base_size = 12,
base_colour = "black",
base_family = "",
parse = FALSE,
padding = unit(c(4, 4), "mm"),
col = base_colour,
lwd=1,
lty=1
){
g <- gridExtra::tableGrob(x,
theme = theme_fun(base_size, base_colour, base_family, parse, padding))
separators <- replicate(ncol(g) - 2,
grid::segmentsGrob(x1 = unit(0, "npc"), gp=gpar(col=col,lwd=lwd,lty=lty)),
simplify=FALSE)
g <- gtable::gtable_add_grob(g, grobs = separators,
t = 2, b = nrow(g), l = seq_len(ncol(g)-2)+2)
ggplot2::ggplot() + ggplot2::annotation_custom(g) + ggplot2::theme_void()
}
simple example:
table_plot(head(iris))
complicated example :
iris2 <- setNames(head(iris)[1:3],c("alpha*integral(xdx,a,infinity)", "this text\nis high", 'alpha/beta'))
table_plot(iris2,
base_size=10,
base_colour="darkred",
base_family = "serif",
parse=TRUE,
theme=ttheme_default,
lwd=3,
lty=2,
col="darkblue")
Related
This is driving me nuts. Have two ggplot objects p and q and use the elegant cowplot::plot_grid function to combine both plots in said grid. However I do get a kind of separation line between the two arranged plots. I use the code below.
library(ggplot2)
library(cowplot)
comb <- plot_grid(p, q, labels = c('A', 'B'),
nrow = 2, ncol = 1,
align = "h",
label_fontfamily = "serif",
greedy = TRUE,
label_size = 12)
comb <- comb + panel_border(remove = TRUE)
save_plot("plot_combined.pdf", comb)
My questions are the following:
How can I remove the separation line?
How can I increase the 'spacing' between the two plots to avoid having the label interfere with the y axis title?
The trick was to adjust my theme as following:
p + theme(plot.background = element_blank()) # This did the trick for me!
You might look at the ggarrange function in the "ggpubr" package. I find it more user friendly than cowplot.
library(ggpubr)
ggarrange(p, q, ncol = 1, nrow = 2, labels = "AUTO")
Here is a sample script using random numbers instead of real elevation data.
library(gridExtra)
library(spatstat) #im function
elevation <- runif(500, 0, 10)
B <- matrix(elevation, nrow = 20, ncol = 25)
Elevation_Map <- im(B)
custom <- colorRampPalette(c("cyan","green", "yellow", "orange", "red"))
plot(Elevation_Map, col = custom(10), main = NULL)
This is the plot and legend that I get:
This is the legend that I am trying to recreate in R (this one made in Word):
I know this is possible and its probably a simple solution but I've tried using some examples I found online to no avail.
This plot (with real elevation data) is an art piece that will be hung in a gallery, with the elevation plot on 1 board and the legend on a separate board. I tried to get R to plot just the plot without the legend using
plot(Elevation_Map, col = custom(10), main = NULL, legend = NULL)
like I have in the past but for some reason it always plots the legend with the plot. As of right now I'm planning on just cropping the .pdf into 2 separate files to achieve this.
Here are two ways of doing it using other packages:
# example data, set seed to reproduce.
set.seed(1); elevation <- runif(500, 0, 10)
B <- matrix(elevation, nrow = 20, ncol = 25)
#Elevation_Map <- im(B)
custom <- colorRampPalette(c("cyan","green", "yellow", "orange", "red"))
1) Using fields package, image.plot(), it is same "base" graphics::image.default() plot but with more arguments for customisation (but couldn't remove the ticks from legend):
library(fields)
image.plot(B, nlevel = 10, col = custom(10),
breaks = 1:11,
lab.breaks = c("Low Elevation", rep("", 9), "High Elevation"),
legend.mar = 10)
2) Using ggplot package, geom_raster function:
library(ggplot2)
library(reshape) # convert matrix to long dataframe: melt
B_melt <- reshape2::melt(B)
head(B_melt)
ggplot(B_melt, aes(X1, X2, fill = value)) +
geom_raster() +
theme_void() +
scale_fill_gradientn(name = element_blank(),
breaks = c(1, 9),
labels = c("Low Elevation", "High Elevation"),
colours = custom(10))
The code in the original post is using the im class from the spatstat package. The plot command is dispatched to plot.im. Simply look at help(plot.im) to figure out how to control the colour ribbon. The relevant argument is ribargs. Here is a solution:
plot(Elevation_Map, col=custom(10), main="",
ribargs=list(at=Elevation_Map$yrange,
labels=c("Low Elevation", "High Elevation"),
las=1))
I use ggplot to make most of my graphics. These can be single panels, or faceted. To make it easier to track revisions, I would like to generate a small label in the corner of the plot that includes some text.
In pseudo code, I am looking for something like this:
# generate the initial plot
p <- ggplot()
# add the label
p + someAnnotationFunction(label = "Version 1.0", x = 1, y = 0,
hjust = "right", vjust = "bottom" )
# print
print(p)
Or: plot my label nestled in the lower right corner of my figure without messing up the existing ggplot graphics.
So far I'm not having any luck finding a solution. This (very interesting) method doesn't work if you have a full m x n table of facets. Methods using gridExtra tend to mess with the plots too much. So, does anyone have a way to add arbitrary text anywhere on a plot that was generated using ggplot?
Here's a worked solution using gridExtra(), based on Baptiste's comment:
require("ggplot2")
require("gridExtra")
# set our working directory
working.dir <- '/Users/aclifton/Documents/projects/Rcode'
setwd(working.dir)
# create a data frame
df <- data.frame(x =runif(100, 1, 10),
y = runif(100, 1, 10))
#create a plot
p <- ggplot(data = df,
aes(x = x,
y = y)) +
geom_point()
print(p)
We now have our plot, and the trick is adding that label and saving the overall plot using ggsave():
# label to show
sub.label = textGrob("Some kind of label",
gp=gpar(fontsize=6),
x = unit(1, "npc"),
hjust = 1,
vjust = 0)
ggsave(filename=file.path(working.dir,'DemoPlot.png'),
plot = arrangeGrob(p,
sub = sub.label,
clip = FALSE),
scale = 1,
width = 6.5,
height = 3.5,
units = c("in"),
dpi = 300)
Which gives you this:
By making a data frame of your annotations, you can add them on top of your plot using geom_text.
note <- data.frame(xVarName = c(1, 5), yVarName = c(1, 10),
text = c("Version 1.0", "April 26, 2014")
p + geom_text(data = anno, aes(label = text))
"Version 1.0" will show up in the bottom left and "April 26, 2014" will show up in the top right.
By making your notes in a separate dataframe, you can add multiple notes to one graph if desired.
The following sample resembles my dataset:
require(randomForest)
alpha = c(1,2,3,4,5,6)
bravo = c(2,3,4,5,6,7)
charlie = c(2,6,5,3,5,6)
mydata = data.frame(alpha,bravo,charlie)
myrf = randomForest(alpha~bravo+charlie, data = mydata, importance = TRUE)
varImpPlot(myrf, type = 2)
I cannot seem to control the placement of the y-axis labels in varImpPlot. I have tried altering the plot parameters (e.g. mar, oma), with no success. I need the y-axis labels shifted to the left in order to produce a PDF with proper label placement.
How can I shift the y-axis labels to the left?
I tried to use adj parameter but it produces a bug. As varImpPlot , use dotchart behind, Here a version using lattice dotplot. Then you can customize you axs using scales parameters.
imp <- importance(myref, class = NULL, scale = TRUE, type = 2)
dotplot(imp, scales=list(y =list(cex=2,
at = c(1,2),
col='red',
rot =20,
axs='i') ,
x =list(cex=2,col='blue')) )
You can extract the data needed to construct the plot out of myref and construct a plot with ggplot. By doing so you have more freedom in tweaking the plot. Here are some examples
library(ggplot2)
str(myrf)
str(myrf$importance)
data <- as.data.frame(cbind(rownames(myrf$importance),round(myrf$importance[,"IncNodePurity"],1)))
colnames(data) <- c("Parameters","IncNodePurity")
data$IncNodePurity <- as.numeric(as.character(data$IncNodePurity))
Standard plot:
(p <- ggplot(data) + geom_point(aes(IncNodePurity,Parameters)))
Rotate y-axis labels:
(p1 <- p+ theme(axis.text.y = element_text(angle = 90, hjust = 1)))
Some more tweaking (also first plot shown here):
(p2 <- p1 + scale_x_continuous(limits=c(3,7),breaks=3:7) + theme(axis.title.y = element_blank()))
Plot that looks like the varImpPlot (second plot shown here) :
(p3 <- p2+ theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
panel.grid.minor.y = element_blank(),
panel.grid.major.y = element_line(colour = 'gray', linetype = 'dashed'),
panel.background = element_rect(fill='white', colour='black')))
Saving to pdf is easy with ggplot:
ggsave("randomforestplot.pdf",p2)
or
ggsave("randomforestplot.png",p2)
p2
p3
Did I understood correctly, that you want to get texts charlie and bravo more left of the boundary of the plot? If so, here's one hack to archive this, based on the modification of the rownames used in plotting:
myrf = randomForest(alpha~bravo+charlie, data = mydata, importance = TRUE)
#add white spaces at the end of the rownames
rownames(myrf$importance)<-paste(rownames(myrf$importance), " ")
varImpPlot(myrf, type = 2)
The adj parameter in dotchart is fixed as 0 (align to right), so that cannot be changed without modifying the code of dotchart:
mtext(labs, side = 2, line = loffset, at = y, **adj = 0**, col = color,
las = 2, cex = cex, ...)
(from dotchart)
EDIT:
You can make another type of hack also. Take the code of dotchart, change the above line to
mtext(labs, side = 2, line = loffset, at = y, adj = adjust_ylab, col = color,
las = 2, cex = cex, ...)
Then add argument adjust_ylab to the argument list, and rename the function as for example dotchartHack. Now copy the code of varImpPlot, find the line which calls dotchart, change the function name to dotchartHack and add the argument adjust_ylab=adjust_ylab to function call, rename the function to varImpPlotHack and add adjust_ylab to this functions argument list. Now you can change the alignment of the charlie and bravo by changing the parameter adjust_ylab:
myrf = randomForest(alpha~bravo+charlie, data = mydata, importance = TRUE)
varImpPlotHack(myrf, type = 2,adjust_ylab=0.5)
From ?par:
The value of adj determines the way in which text strings are
justified in text, mtext and title. A value of 0 produces
left-justified text, 0.5 (the default) centered text and
right-justified text. (Any value in [0, 1] is allowed, and on most
devices values outside that interval will also work.)
I have recently started using the grid.table function from the gridExtra package to turn tabular data into png image files for use on the web. I've been delighted with it so far as it produces very good-looking output by default, sort of like a ggplot2 for tables. Like the person who asked this question I would love to see the ability to specify the justification for individual columns but that would be icing on what is an already more-ish cake.
My question is whether it is possible to add text around a grid.table so that I can give plotted tables a title and a footnote. It seems to me this should be feasible, but I don't know enough about grid graphics to be able to work out how to add grobs to the table grob. For example, this code:
require(gridExtra)
mydf <- data.frame(Item = c('Item 1','Item 2','Item 3'),
Value = c(10,15,20), check.names = FALSE)
grid.table(mydf,
gpar.coretext=gpar(fontsize = 16),
gpar.coltext = gpar(fontsize = 16),
gpar.rowtext = gpar(fontsize = 16),
gpar.corefill = gpar(fill = "blue", alpha = 0.5, col = NA),
h.even.alpha = 0.5,
equal.width = FALSE,
show.rownames = FALSE,
show.vlines = TRUE,
padding.h = unit(15, "mm"),
padding.v = unit(8, "mm")
)
generates this plot:
when I would really like to be able to do something like the following in code rather than by editing the image with another application:
To place text close to the table you'll want to evaluate the table size first,
library(gridExtra)
d <- head(iris)
table <- tableGrob(d)
grid.newpage()
h <- grobHeight(table)
w <- grobWidth(table)
title <- textGrob("Title", y=unit(0.5,"npc") + 0.5*h,
vjust=0, gp=gpar(fontsize=20))
footnote <- textGrob("footnote",
x=unit(0.5,"npc") - 0.5*w,
y=unit(0.5,"npc") - 0.5*h,
vjust=1, hjust=0,gp=gpar( fontface="italic"))
gt <- gTree(children=gList(table, title, footnote))
grid.draw(gt)
Edit (17/07/2015) With gridExtra >=2.0.0, this approach is no longer suitable. tableGrob now returns a gtable, which can be more easily customised.
library(gridExtra)
d <- head(iris)
table <- tableGrob(d)
library(grid)
library(gtable)
title <- textGrob("Title",gp=gpar(fontsize=50))
footnote <- textGrob("footnote", x=0, hjust=0,
gp=gpar( fontface="italic"))
padding <- unit(0.5,"line")
table <- gtable_add_rows(table,
heights = grobHeight(title) + padding,
pos = 0)
table <- gtable_add_rows(table,
heights = grobHeight(footnote)+ padding)
table <- gtable_add_grob(table, list(title, footnote),
t=c(1, nrow(table)), l=c(1,2),
r=ncol(table))
grid.newpage()
grid.draw(table)
If you want just the title (no footnote), here is a simplified version of #baptiste's example:
title <- textGrob("Title", gp = gpar(fontsize = 50))
padding <- unit(0.5,"line")
table <- gtable_add_rows(
table, heights = grobHeight(title) + padding, pos = 0
)
table <- gtable_add_grob(
table, list(title),
t = 1, l = 1, r = ncol(table)
)
grid.newpage()
grid.draw(table)