Align panel.background instead of plot.background with document margins - ggplot2

I would like to have plots generated by ggplot2 inserted into a LaTeX document with the panel as wide as \textwidth (or \columnwidth in a two column document). I have the following solution:
\documentclass{article}
\usepackage{lipsum, graphicx}
<<knitrOpts, echo=FALSE>>=
knitr::opts_chunk$set(echo = FALSE,
fig.show = 'hide',
fig.width=general_fig_width <- 5,
fig.height=3,
out.width = out_width <- "5in",
out.height="3in"
)
#
\usepackage{geometry}
\setlength{\textwidth}{\Sexpr{out_width}}
<<loadPackages>>=
library(ggplot2)
library(dplyr)
library(grid)
#
\begin{document}
<<plot>>=
diamonds %>%
sample_frac(0.3) %>%
ggplot(aes(x = carat, y = price)) +
geom_point() +
theme_dark() +
theme(plot.margin = unit(c(0,0,0,0), "pt"))
grid.ls(view=TRUE,grob=FALSE)
current.vpTree()
seekViewport('panel.3-4-3-4')
a <- convertWidth(unit(1,'npc'), 'inch', TRUE)
width_factor <- general_fig_width / a
#
\lipsum
\begin{figure}[t]
\makebox[\textwidth][r]{\includegraphics[width=\Sexpr{width_factor}\textwidth]{figure/plot-1}}
\end{figure}
\lipsum
\end{document}
However, the solution does not work when a legend is added:
diamonds %>%
sample_frac(0.3) %>%
ggplot(aes(x = carat, y = price, color = price)) +
geom_point() +
theme_dark() +
theme(plot.margin = unit(c(0,0,0,0), "pt"))
The legend messes up the alignment. Setting the pos argument in \makebox won't work as the background is off-centre. I understand I could put the legend atop the chart, but I'd prefer to have the option to have the legend intrude into the margin.

you'll probably find it easier to query sizes if you work with the gtable,
---
title: "Untitled"
header-includes:
- \usepackage{lipsum}
output:
pdf_document:
fig_caption: yes
fig_crop: no
keep_tex: yes
geometry: width=5in
---
```{r setup, include=FALSE}
library(ggplot2)
library(dplyr)
library(grid)
library(knitr)
general_fig_width <- 5
```
```{r plot, fig.show=FALSE}
p <- diamonds %>%
sample_frac(0.3) %>%
ggplot(aes(x = carat, y = price, color = price)) +
geom_point() +
theme_dark() +
theme(plot.margin = unit(c(0,0,0,0), "pt"))
g <- ggplotGrob(p)
if(getRversion() < "3.3.0"){
g$widths <- grid:::unit.list(g$widths)
g$widths[4] <- list(unit(general_fig_width, "in"))
} else {
g$widths[4] <- unit(general_fig_width, "in")
}
fig_width <- convertWidth(sum(g$widths), "in", valueOnly = TRUE)
left_width <- convertWidth(sum(g$widths[1:3]), "in", valueOnly = TRUE)
ggsave('plot-tmp.pdf', width=fig_width, height=2)
```
\begin{figure}[!hb]
\hspace{`r -left_width`in}\includegraphics[width=`r fig_width`in]{plot-tmp}
\end{figure}
\lipsum[2]

Related

How to delete NA from the graph

I'm still learning R and I'm not sure why there is NA data in my graph. Considering that I have used the table function to check the variables in the column.
graph
Any suggestions to remove the NA variable in my graph?
Please find below sample of code(not actual dataset):
*Install and load relevant packages
install.packages("tidyverse")
install.packages("lubridate")
install.packages("ggplot2")
install.packages("tibble")
library(tidyverse)
library(lubridate)
library(ggplot2)
library(tibble)
library(dplyr)
*data frame
all_trips <- tribble(~start, ~end, ~start_name, ~type,
"2020-03-22 03:20:20", "2020-03-22 04:10:15", "A", "member",
"2020-03-25 01:01:07", "2020-03-25 05:09:45", NA, "member",
"2020-03-26 07:09:55", "2020-03-26 08:10:20", "B", "casual",
"2020-03-29 09:10:30", "2020-03-29 09:00:20", "A", "casual",
"2020-03-30 11:09:18", "2020-03-30 03:40:10", "B", "member")
*generate new columns
all_trips$date <- as.Date(all_trips$start) #The default format is yyyy-mm-dd
all_trips$month <- format(as.Date(all_trips$date), "%m")
all_trips$day <- format(as.Date(all_trips$date), "%d")
all_trips$year <- format(as.Date(all_trips$date), "%Y")
all_trips$day_of_week <- format(as.Date(all_trips$date), "%A")
all_trips$ride_length <- difftime(all_trips$end,all_trips$start)
is.factor(all_trips$ride_length)
all_trips$ride_length <- as.numeric(as.character(all_trips$ride_length))
is.numeric(all_trips$ride_length)
*data cleaning
all_trips_v2 <- all_trips[!(all_trips$start_name == "NA" |
all_trips$ride_length<0),]
*data viz
all_trips_v2 %>%
mutate(weekday = wday(start, label = TRUE)) %>% #creates weekday field using wday()
group_by(type, weekday) %>% #groups by usertype and weekday
summarise(number_of_rides = n() #calculates the number of rides and average duration
,average_duration = mean(ride_length)) %>% # calculates the average duration
arrange(type, weekday) %>% # sorts
ggplot(aes(x = weekday, y = number_of_rides, fill = type)) +
geom_col(position = "dodge", na.rm = TRUE) +
scale_x_discrete(na.translate = FALSE)
Bar Chart:
Click here
Adding na.rmand na.translate arguments will remove missing values from bar chart without a warning message as shown here:
tibble(x = rep(c('One', 'Two', 'Two', NA),2), Group=rep(c("A","B"),each=4)) %>%
ggplot(aes(x, fill=Group)) +
labs(title="Sample Group Bar Chart with NA's Removed") +
geom_bar(stat="Count", position=position_dodge(), na.rm = TRUE) +
scale_x_discrete(na.translate = FALSE)

How to draw plots and have specific name for each plot

I draw plots stored in list mp , how to make mp[["A"]] plot title is A_plot? (And mp[["B"]] plot title is 'B_plot')
title=paste0(names(.),'_plot') can't get what i want
library(tidyverse)
test_data <- data.frame(
category=c('A','A','A','B','B','B'),
price=c(1,1,2,3,2,2),
amount=c(1:6)
) %>% split(.$category)
mp <- map(test_data,~ ggplot(.,aes(x=price,y=amount))+
geom_point()+labs(title=paste0(names(.),'_plot')))
mp[["A"]]
Using purrr::imap you could do:
library(tidyverse)
mp <- imap(test_data, ~ ggplot(.x, aes(x = price, y = amount)) +
geom_point() +
labs(title = paste0(.y, "_plot")))
mp[["A"]]

Add space argument to facet_wrap

facet_wrap() has been recognized for not having a space = "free" argument (https://github.com/tidyverse/ggplot2/issues/2933). This can causes spacing issues on the y-axis of plots.
Create the above figure using the following code:
library(tidyverse)
p <-
mtcars %>%
rownames_to_column() %>%
ggplot(aes(x = disp, y = rowname)) + geom_point() +
facet_wrap(~ carb, ncol = 1, scales = "free_y")
facet_grid on the other hand has a space = "free" argument. Allowing for nice y-axis spacing.
Create the above figure using the following code:
p <-
mtcars %>%
rownames_to_column() %>%
ggplot(aes(x = disp, y = rowname)) + geom_point() +
facet_grid(carb ~ ., scales = "free_y", space = "free_y")
The issue with this is that the label is on the side, not the top. I sometimes have longer facet labels and few rows in the facet. This means the facet label gets cut off.
There is a solution from the ggforce package (comment by ilarischeinin on https://github.com/tidyverse/ggplot2/issues/2933).
p <-
mtcars %>%
rownames_to_column() %>%
ggplot(aes(x = disp, y = rowname)) + geom_point()
p + ggforce::facet_col(vars(carb), scales = "free_y", space = "free")
But, there are limitations leaving ggplot2. For example, I ultimately want a two column figure, and this functionality does not seem possible with ggforce. Is there any way to produce the same result using facet_wrap() so that I can utilize the ncol() argument?
Here is a potential workaround based on https://stackoverflow.com/a/29022188/12957340 :
library(tidyverse)
library(gtable)
library(grid)
p1 <- mtcars %>%
rownames_to_column() %>%
ggplot(aes(x = disp, y = rowname)) + geom_point() +
facet_grid(carb ~ ., scales = "free_y", space = "free_y") +
theme(panel.spacing = unit(1, 'lines'),
strip.text.y = element_text(angle = 0))
gt <- ggplotGrob(p1)
panels <-c(subset(gt$layout, grepl("panel", gt$layout$name), se=t:r))
for(i in rev(panels$t-1)) {
gt = gtable_add_rows(gt, unit(0.5, "lines"), i)
}
panels <-c(subset(gt$layout, grepl("panel", gt$layout$name), se=t:r))
strips <- c(subset(gt$layout, grepl("strip-r", gt$layout$name), se=t:r))
stripText = gtable_filter(gt, "strip-r")
for(i in 1:length(strips$t)) {
gt = gtable_add_grob(gt, stripText$grobs[[i]]$grobs[[1]], t=panels$t[i]-1, l=5)
}
gt = gt[,-6]
for(i in panels$t) {
gt$heights[i-1] = unit(0.8, "lines")
gt$heights[i-2] = unit(0.2, "lines")
}
grid.newpage()
grid.draw(gt)
Created on 2021-12-15 by the reprex package (v2.0.1)
It's not clear to me what you mean by "I ultimately want a two column figure", but if you can come up with an example to illustrate your 'ultimate' expected outcome I can try to adapt this approach and see if it will work or not.

double geom_bar, how to get the values for each bar

I have a ggplot of countries (X axis) over two different time periods (Y axis), so double bar for each country.
I would like to see the values of each bar. I used geom_text but I get the values on the same line so they are not in place. How can I use geom_text for this type of plot ?
Rcountry %>%
gather("Type", "Value",-Country) %>%
ggplot(aes(Country, Value, fill = Type)) +
geom_bar(position = "dodge", stat = "identity") +
coord_flip()+
theme_minimal()+scale_fill_grey()+
theme(legend.position="bottom")+
theme(legend.title = element_blank())+
scale_fill_manual(values=c("darkslategray4", "darkslategrey"))+
labs(x="Country", y="Stock of robots per thousands worker in '000")+
geom_text(aes(label=c(X2010, X2018)), size=3.5)```
Thank you
This can be achieved by adding position = position_dodge(.9) to geom_text, i.e. you have to the positioning used in geom_bar to geom_text to get the labels right. Using mtcars as example data, try this:
library(ggplot2)
library(dplyr)
mtcars2 <- mtcars %>%
group_by(cyl, gear) %>%
summarise(mpg = mean(mpg)) %>%
ungroup()
ggplot(mtcars2, aes(x = factor(cyl), mpg, fill = factor(gear))) +
geom_bar(position = "dodge", stat = "identity") +
theme_minimal() +
scale_fill_grey() +
theme(legend.position="bottom")+
theme(legend.title = element_blank())+
labs(x="Country", y="Stock of robots per thousands worker in '000")+
geom_text(aes(label = mpg), position = position_dodge(.9), size=3.5) +
coord_flip()
Created on 2020-04-15 by the reprex package (v0.3.0)

ggplot grobs align with tableGrob

I'm having difficulty to find solution for aligning ggplot grob and table grob. I tried to follow the instruction here but still didn't give the results I wanted.
library(grid)
library(gridExtra)
library(ggplot2)
library(tibble)
library(gtable)
dat <- tibble::rownames_to_column(mtcars, "car") #convert rownames to first col
plot1 <- ggplot(dat, aes(car, mpg)) +
geom_bar(stat = "identity") +
coord_flip()
g1 <- ggplotGrob(plot1)
tb1 <- tableGrob(dat$cyl)
g1 <- gtable_add_cols(g1, unit(0.2, "npc"))
g1 <- gtable_add_grob(g1, grobs = tb1, t=3, l=ncol(g1), b=6, r=ncol(g1))
grid.newpage()
grid.draw(g1)
I would like that each cell in the table be aligned to related bar in histogram, but still couldn't understand how the t,l,b,r be implemented from the layout.This is the output I got
I had a similar question as above when trying to make something like a forestplot in R using ggplot2 and didn't find any of the other solutions fit my needs. The answer above didn't work for me - the table didn't show up. So I hacked together a codewise not that pretty solution, but I actually kind of like the cleanliness visual output.
The things I like about this solution are:
I aligned a set of custom text not in a table, but just in a figure on the right, where the alignment matched for each text entry and each label in the figure.
I used a centered ggtitle to align a "column heading" above each set of text. These could be strings of any kind (in my actual use, I had point estimates and confidence intervals).
library(gridExtra)
library(ggplot2)
dat <- data.frame(
label = c("A", "B", "C"),
point_est = c(1,2,3),
lb_ci = c(.5, 1.5, 2.5),
ub_ci = c(1.5, 2.5, 3.5),
n = c(50, 100, 150),
total = c(75, 150, 200)
)
plot1 <- ggplot(dat, aes(x=point_est, y=label)) +
geom_point() +
geom_errorbarh(aes(xmin=lb_ci, xmax=ub_ci), height=.5) +
ggtitle("Some measure") +
ylab(NULL) + xlab("some effect estimate")
tab_base <- ggplot(dat, aes(y=label)) +
ylab(NULL) + xlab(" ") +
theme(plot.title = element_text(hjust = 0.5, size=12), ## centering title on text
axis.text.x=element_text(color="white"), ## need text to be printed so it stays aligned with figure but white so it's invisible
axis.line=element_blank(),
axis.text.y=element_blank(),axis.ticks=element_blank(),
axis.title.y=element_blank(),legend.position="none",
panel.background=element_blank(),panel.border=element_blank(),panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),plot.background=element_blank())
tab1 <- tab_base +
geom_text(aes(x=1, label=n)) +
ggtitle("n")
tab2 <- tab_base +
geom_text(aes(x=1, label=total)) +
ggtitle("total")
lay <- matrix(c(1,1,1,1,1,1,2,3), nrow=1)
grid.arrange(plot1, tab1, tab2, layout_matrix = lay)
By default the cell heights have absolute sizes to accommodate the text, but you can change them to relative units so that they scale with the plot panel,
library(grid)
library(gridExtra)
library(ggplot2)
library(tibble)
library(gtable)
dat <- tibble::rownames_to_column(mtcars, "car") #convert rownames to first col
plot1 <- ggplot(dat, aes(car, mpg)) +
geom_bar(stat = "identity") +
coord_flip()
g1 <- ggplotGrob(plot1)
tb1 <- tableGrob(dat$cyl, theme = ttheme_default(10))
tb1$heights = unit(rep(1/(nrow(tb1)), nrow(tb1)), "npc")
tb1$widths = unit.pmax(tb1$widths, unit(2, "lines"))
g1 <- gtable_add_cols(g1, sum(tb1$widths))
g1 <- gtable_add_grob(g1, grobs = tb1, t=6, l=ncol(g1), b=6, r=ncol(g1))
grid.newpage()
grid.draw(g1)