In the following plot:
library(ggplot2)
test <- data.frame(Depth=c(rep(c(0,10,20),4)),
Core=c(rep("A", 6), rep("B",6)),
Variable=c(rep("Treat1",3),rep("Treat2",3), rep("Treat1",3),rep("Treat2",3)),
Value=runif(12,0,1))
ggplot(test, aes(Value, Depth, col=Variable, shape=Core, lty=Core))+
geom_path(aes(group=interaction(Variable, Core))) +
geom_point(aes(group=interaction(Variable, Core)))+
theme_bw()+
guides(colour = guide_legend(aes.override=list(linetype = "solid")))
is it possible with remove the shapes from the colour-based legend (set to "Variable"), as i tried with aes.overide in guides?
My real life example produces this legend:
and I want to remove the shapes from the left legend; in fact I want to replace the current legend keys (lines and shapes) with filled boxes. Since the aes contains an interaction-argument, I fear my attempt to manipulate the legend via colour=guide_legend is futile.
Use override.aes instead of aes.override where you specify linetype = 0, shape = 15 (boxes):
ggplot(test, aes(Value, Depth,
color = Variable, shape = Core, lty = Core))+
geom_path(aes(group = interaction(Variable, Core))) +
geom_point(aes(group = interaction(Variable, Core)))+
theme_bw()+
guides(colour = guide_legend(override.aes=list(shape = 15, size = 5, linetype = 0)))
Result:
Related
I'm trying to use ggplot2 to make some sort of timeline using values from a dataframe (df). I've managed to plot the data exactly how I want it (the different colored line segments connecting the x-marks in this exact order, i.e., from left to right: 'early', 'unknown', 'late', 'sub'). The startpoint and endpoint columns in the dataframe are used to define the positions of the points and line segments.
The problem is that the legend doesn't show the color of the 'x' icons, they are just grey. I've tried adding scale_color_manual() and scale_fill_manual() commands but they don't seem to change anything. The legend does display the correct color when I change the shape to shape = 21, however, I really want the shape to be 4 (x icons). I don't care about the shape of the legend though but scale_shape_manual() again didn't change anything about the legend.
I have also tried placing different color arguments inside and outside the aes() argument of ggplot(), geom_segment() and/or geom_point().
How can I make the icons from the legend show the correct color?
Below I added a piece of code to reproduce the problem.
library(ggplot2)
library(RColorBrewer)
## Define dataframe
df <- data.frame(Var = c("sub","late","unknown","early"),
Time = c(10,267,0,1256),
Endpoint = c(1533,1523,1256,1256),
Startpoint = c(1523,1256,1256,0))
colorscheme <- RColorBrewer::brewer.pal(9, "Set1")[c(1,4,2,3)]
## Make plot
ggplot(df, aes(x="", y=Endpoint, fill=Var), color =colorscheme) +
geom_segment( aes(x="", xend="", y=Startpoint, yend=Endpoint), color = colorscheme) +
geom_point(aes(x="", y=Endpoint),size=5, shape=4 , color = colorscheme) +
coord_flip()
Thanks in advance for any suggestions!
You should use color instead of fill. To remove the line from the legend, use guides(color = guide_legend(override.aes = list(linetype = 0))) or use show.legend = F in geom_segment.
Also, arguments passed in ggplot need not to be repeated afterward.
ggplot(df, aes(x="", y=Endpoint, color=Var), colorscheme) +
geom_segment(aes(xend="", y=Startpoint, yend=Endpoint)) +
geom_point(size=5, shape=4) +
coord_flip() +
guides(color = guide_legend(override.aes = list(linetype = 0)))
#or
ggplot(df, aes(x="", y=Endpoint, color=Var), colorscheme) +
geom_segment(aes(xend="", y=Startpoint, yend=Endpoint)) +
geom_point(size=5, shape=4) +
coord_flip()
Try this:
ggplot(df, aes(x = "", y = Endpoint, color = Var), colorscheme) +
geom_segment(aes(x = "", xend = "", y = Startpoint, yend = Endpoint), show.legend = FALSE) +
geom_point(aes(x = "", y = Endpoint), size = 5, shape = 4) +
coord_flip()
In this way legend will show only X
I have data where each point lays on a spectrum between two centroids. I have generated a color for each point by specifying a color for each centroid, then setting the color of each point as a function of its position between its two centroids. I used this to manually specify colors for each point and plotted the data in the following way:
lb.plot.dat <- data.frame('UMAP1' = lb.umap$layout[,1], 'UMAP2' = lb.umap$layout[,2],
'sample' = as.factor(substr(colnames(lb.vip), 1, 5)),
'fuzzy.class' = color.vect))
p3 <- ggplot(lb.plot.dat, aes(x = UMAP1, y = UMAP2)) + geom_point(aes(color = color.vect)) +
ggtitle('Fuzzy Classification') + scale_color_identity()
p3 + facet_grid(cols = vars(sample)) + theme(legend.) +
ggsave(filename = 'ref-samps_bcell-vip-model_fuzzy-class.png', height = 8, width = 16)
(color.vect is the aforementioned vector of colors for each point in the plot)
I would like to generate a legend of this plot that gives the color used for each centroid. I have a named vector class.cols that contains the colors used for each centroid and is named according to the corresponding class.
Is there a way to transform this vector into a legend for the plot even though it is not explicitly used in the plotting call?
You can turn on legend drawing in scale_color_identity() by setting guide = "legend". You'll have to specify the breaks and labels in the scale function so that the legend correctly states what each color represents, and not just the name of the color.
library(ggplot2)
df <- data.frame(x = 1:3, y = 1:3, color = c("red", "green", "blue"))
# no legend by default
ggplot(df, aes(x, y, color = color)) +
geom_point() +
scale_color_identity()
# legend turned on
ggplot(df, aes(x, y, color = color)) +
geom_point() +
scale_color_identity(guide = "legend")
Created on 2019-12-15 by the reprex package (v0.3.0)
I have a bunch of data for people touching bacteria for up to 5 touches. I'm comparing how much they pick up with and without gloves. I'd like to plot the mean by the factor NumberContacts and colour it red. E.g. the red dots on the following graphs.
So far I have:
require(tidyverse)
require(reshape2)
Make some data
df<-data.frame(Yes=rnorm(n=100),
No=rnorm(n=100),
NumberContacts=factor(rep(1:5, each=20)))
Calculate the mean for each group= NumberContacts
centroids<-aggregate(data=melt(df,id.vars ="NumberContacts"),value~NumberContacts+variable,mean)
Get them into two columns
centYes<-subset(centroids, variable=="Yes",select=c("NumberContacts","value"))
centNo<-subset(centroids, variable=="No",select="value")
centroids<-cbind(centYes,centNo)
colnames(centroids)<-c("NumberContacts","Gloved","Ungloved")
Make an ugly plot.
ggplot(df,aes(x=gloves,y=ungloved)+
geom_point()+
geom_abline(slope=1,linetype=2)+
stat_ellipse(type="norm",linetype=2,level=0.975)+
geom_point(data=centroids,size=5,color='red')+
#stat_summary(fun.y="mean",colour="red")+ doesn't work
facet_wrap(~NumberContacts,nrow=2)+
theme_classic()
Is there a more elegant way by using stat_summary? Also How can I change the look of the boxes at the top of my graphs?
stat_summary is not an option because (see ?stat_summary):
stat_summary operates on unique x
That is, while we can take a mean of y, x remains fixed. But we may do something else that is very concise:
ggplot(df, aes(x = Yes, y = No, group = NumberContacts)) +
geom_point() + geom_abline(slope = 1, linetype = 2)+
stat_ellipse(type = "norm", linetype = 2, level = 0.975)+
geom_point(data = df %>% group_by(NumberContacts) %>% summarise_all(mean), size = 5, color = "red")+
facet_wrap(~ NumberContacts, nrow = 2) + theme_classic() +
theme(strip.background = element_rect(fill = "black"),
strip.text = element_text(color = "white"))
which also shows that to modify the boxes above you want to look at strip elements of theme.
I am trying to recreate this visualization of a bubble chart using ggplot2 (I have found the code for doing this in R, but not with the ggplot2 package). This is what I have so far. There are some other errors with my code at the moment, but I want to have the legend show concentric circles for size, versus circles shown in rows. Thanks for your help!
Original visualization:
My reproduction:
My (simplified) code:
crime <-
read.csv("http://datasets.flowingdata.com/crimeRatesByState2005.tsv",
header=TRUE, sep="\t")
ggplot(crime,
mapping= aes(x=murder, y=burglary))+
geom_point(aes(size=population), color="red")+
geom_text(aes(label=state.name), show.legend=FALSE, size=3)+
theme(legend.position = c(0.9, 0.2))
Here's an approach where we build the legend as imagined from scratch.
1) This part slightly tweaks your base chart.
Thank you for including the source data. I missed that earlier and have edited this answer to use it. I switched to a different point shape so that we can specify both outside border (color) as well as interior fill.
gg <- ggplot(crime,
mapping= aes(x=murder, y=burglary))+
geom_point(aes(size=population), shape = 21, color="white", fill = "red")+
ggrepel::geom_text_repel(aes(label = state.name),
size = 3, segment.color = NA,
point.padding = unit(0.1, "lines")) +
theme_classic() +
# This scales area to size (not radius), specifies max size, and hides legend
scale_size_area(max_size = 20, guide = FALSE)
2) Here I make another table to use for the concentric legend circles
library(dplyr); library(ggplot2)
legend_bubbles <- data.frame(
label = c("3", "20", "40m"),
size = c(3E6, 20E6, 40E6)
) %>%
mutate(radius = sqrt(size / pi))
3) This section adds the legend bubbles, text, and title.
It's not ideal, since different print sizes will require placement tweaks. But it seems like it'd get complicated to get into the underlying grobs with ggplot_build to extract and use those sizing adjustments...
gg + geom_point(data = legend_bubbles,
# The "radius/50" was trial and error. Better way?
aes(x = 8.5, y = 250 + radius/50, size = size),
shape = 21, color = "black", fill = NA) +
geom_text(data = legend_bubbles, size = 3,
aes(x = 8.5, y = 275 + 2 * radius/50, label = label)) +
annotate("text", x = 8.5, y = 450, label = "Population", fontface = "bold")
I would like to draw a chart with ggplot for a couple of model accuracies. The detail of the plotted result doesn't matter, however, I've a problem to fill the geom_point objects.
A sample file can be found here: https://ufile.io/z1z4c
My code is:
library(ggplot2)
library(ggthemes)
Palette <- c('#A81D35', '#085575', '#1DA837')
results <- read.csv('test.csv', colClasses=c('factor', 'factor', 'factor', 'numeric'))
results$dates <- factor(results$dates, levels = c('01', '15', '27'))
results$pocd <- factor(results$pocd, levels = c('without POCD', 'with POCD', 'null accuracy'))
results$model <- factor(results$model, levels = c('SVM', 'DT', 'RF', 'Ada', 'NN'))
ggplot(data = results, group = pocd) +
geom_point(aes(x = dates, y = acc,
shape = pocd,
color = pocd,
fill = pocd,
size = pocd)) +
scale_shape_manual(values = c(0, 1, 3)) +
scale_color_manual(values = c(Palette[1], Palette[2], Palette[3])) +
scale_fill_manual(values = c(Palette[1], Palette[2], Palette[3])) +
scale_size_manual(values = c(2, 2, 1)) +
facet_grid(. ~ model) +
xlab('Date of knowledge') +
ylab('Accuracy') +
theme(legend.position = 'right',
legend.title = element_blank(),
axis.line = element_line(color = '#DDDDDD'))
As a result I get unfilled circles and squares. How can I fix it, so that the squares and circles are filled with the specfic color?
Additional question: I would like to add a geom_line to the graph, connecting the three points in each group. However, I fail to adjust linetype and width. It always take the values of scale_*_manual, which is very adverse especially in the case of size.
Thanks for helping!
You need to change the shapes specified, like so:
scale_shape_manual(values = c(21,22,23)) +
For your additional question, that should be solved if you set aes(size=) in the first part of your code (under ggplot(data=...) and then manually specify size=1 under geom_line as +geom_line(size=1....`