My question is that I want to add the categorical variables' legends onto the graph but somehow when I used "topright", it did not work for me (see the image below). Basically my idea is to fill the blank area with the legends for my categorical variables on the side of the heatmap. My codes look like
heatmap.3(performance, Colv =NA,RowSideColors=row_annotation,col=my_palette)
par(lend = 1) # square line ends for the color legend
legend("topright", # location of the legend on the heatmap plot
legend = c("category1", "category2", "category3"), # category labels
col = c("gray", "blue", "black"), # color key
lty= 1, # line style
lwd = 10 # line width
)
Also I want to put multiple legend onto the plot but don't know how to specify their positions using x and y as there are no coordinates in my plot.
Thank you so much!
A simple fix to your problem would be to use the option inset=# (where # is some floating point number with a comma after it) following your "topright" specification after its respective comma, which would indicate how to place your legend relative to your graph.
Instead of specifying the default position "topright", perhaps you may want to try restructuring your code in a more personally customized manner, namely utilizing an x-y axis approach, such as for instance use :
dev.new(xpos=#,ypos=#)
Or you may also consider using:
legend.position=c(#,#)
Try these options, even though you say you have no access to coordinates, which is rare for graphical utilities in R, but may well be a future edit to heatmap.3. You could also use a fancy R utility called locator(1) to point and click with your mouse where you want to see your legend.
In general, the legend option is formally defined as:
legend(location, title, legend, ...)
If you have any more questions about the legend utility in R, please type in help(legend) in your R command line (in R Studio, for instance, if you use that).
To address your question on multiple legends, please consult: Plotting multiple legends
Related
I have a curve, for instance
y_curve=c(1,2,5,6,9,1).
and the colors for each curve point
colors=c("#0000FF","#606060","#606060","#FF0000","#FF0000","#FF0000").
In theory I want to plot a curve where the first half has one color (except for the first point which is blue) and the second half has another color. In my example the dataset has more than 3000 observations so it makes sense.
For some reason, if I plot the data just using the command
plot(y_curve,col=colors), the color of points is plotted corrently.
Nevertheless, if I add the option type="l", the plotted curve has only one color - the blue, which is the first color in the vector colors ("#0000FF").
Does anyone know what am I doing wrong?
So the code is
y_curve=c(1,2,5,6,9,1)
colors=c("#0000FF","#606060","#606060","#FF0000","#FF0000","#FF0000")
plot(y_curve,col=colors,type="l")
Thank you all in advance.
I avoid using ggplot since this part of code is inside an already complicated function and I prefer using the base R commands.
The line option for the plot function does not accept multiple colors.
There is the segments() function that we can use to manually draw in each separate segment individually with a unique color.
y_curve=c(1,2,5,6,9,1)
colors=c("#0000FF","#606060","#606060","#FF0000","#FF0000","#FF0000")
#create a mostly blank plot
plot(y_curve,col=NA)
# Use this to show the points:
#plot(y_curve,col=colors)
#index variable
x = seq_along(y_curve)
#draw the segments
segments(head(x,-1), head(y_curve,-1), x[-1], y_curve[-1], type="l", col=colors)
This answer is based on the solution to this question:
How do I plot a graph in R, with the first values in one colour and the next values in another colour?
I am making a scatter plot of two variables and would like to colour the points by a factor variable. Here is some reproducible code:
data <- iris
plot(data$Sepal.Length, data$Sepal.Width, col=data$Species)
This is all well and good but how do I know what factor has been coloured what colour??
data<-iris
plot(data$Sepal.Length, data$Sepal.Width, col=data$Species)
legend(7,4.3,unique(data$Species),col=1:length(data$Species),pch=1)
should do it for you. But I prefer ggplot2 and would suggest that for better graphics in R.
The command palette tells you the colours and their order when col = somefactor. It can also be used to set the colours as well.
palette()
[1] "black" "red" "green3" "blue" "cyan" "magenta" "yellow" "gray"
In order to see that in your graph you could use a legend.
legend('topright', legend = levels(iris$Species), col = 1:3, cex = 0.8, pch = 1)
You'll notice that I only specified the new colours with 3 numbers. This will work like using a factor. I could have used the factor originally used to colour the points as well. This would make everything logically flow together... but I just wanted to show you can use a variety of things.
You could also be specific about the colours. Try ?rainbow for starters and go from there. You can specify your own or have R do it for you. As long as you use the same method for each you're OK.
Like Maiasaura, I prefer ggplot2. The transparent reference manual is one of the reasons.
However, this is one quick way to get it done.
require(ggplot2)
data(diamonds)
qplot(carat, price, data = diamonds, colour = color)
# example taken from Hadley's ggplot2 book
And cause someone famous said, plot related posts are not complete without the plot, here's the result:
Here's a couple of references:
qplot.R example,
note basically this uses the same diamond dataset I use, but crops the data before to get better performance.
http://ggplot2.org/book/
the manual: http://docs.ggplot2.org/current/
There are two ways that I know of to color plot points by factor and then also have a corresponding legend automatically generated. I'll give examples of both:
Using ggplot2 (generally easier)
Using R's built in plotting functionality in combination with the colorRampPallete function (trickier, but many people prefer/need R's built-in plotting facilities)
For both examples, I will use the ggplot2 diamonds dataset. We'll be using the numeric columns diamond$carat and diamond$price, and the factor/categorical column diamond$color. You can load the dataset with the following code if you have ggplot2 installed:
library(ggplot2)
data(diamonds)
Using ggplot2 and qplot
It's a one liner. Key item here is to give qplot the factor you want to color by as the color argument. qplot will make a legend for you by default.
qplot(
x = carat,
y = price,
data = diamonds,
color = diamonds$color # color by factor color (I know, confusing)
)
Your output should look like this:
Using R's built in plot functionality
Using R's built in plot functionality to get a plot colored by a factor and an associated legend is a 4-step process, and it's a little more technical than using ggplot2.
First, we will make a colorRampPallete function. colorRampPallete() returns a new function that will generate a list of colors. In the snippet below, calling color_pallet_function(5) would return a list of 5 colors on a scale from red to orange to blue:
color_pallete_function <- colorRampPalette(
colors = c("red", "orange", "blue"),
space = "Lab" # Option used when colors do not represent a quantitative scale
)
Second, we need to make a list of colors, with exactly one color per diamond color. This is the mapping we will use both to assign colors to individual plot points, and to create our legend.
num_colors <- nlevels(diamonds$color)
diamond_color_colors <- color_pallet_function(num_colors)
Third, we create our plot. This is done just like any other plot you've likely done, except we refer to the list of colors we made as our col argument. As long as we always use this same list, our mapping between colors and diamond$colors will be consistent across our R script.
plot(
x = diamonds$carat,
y = diamonds$price,
xlab = "Carat",
ylab = "Price",
pch = 20, # solid dots increase the readability of this data plot
col = diamond_color_colors[diamonds$color]
)
Fourth and finally, we add our legend so that someone reading our graph can clearly see the mapping between the plot point colors and the actual diamond colors.
legend(
x ="topleft",
legend = paste("Color", levels(diamonds$color)), # for readability of legend
col = diamond_color_colors,
pch = 19, # same as pch=20, just smaller
cex = .7 # scale the legend to look attractively sized
)
Your output should look like this:
Nifty, right?
The col argument in the plot function assign colors automatically to a vector of integers. If you convert iris$Species to numeric, notice you have a vector of 1,2 and 3s So you can apply this as:
plot(iris$Sepal.Length, iris$Sepal.Width, col=as.numeric(iris$Species))
Suppose you want red, blue and green instead of the default colors, then you can simply adjust it:
plot(iris$Sepal.Length, iris$Sepal.Width, col=c('red', 'blue', 'green')[as.numeric(iris$Species)])
You can probably see how to further modify the code above to get any unique combination of colors.
The lattice library is another good option. Here I've added a legend on the right side and jittered the points because some of them overlapped.
xyplot(Sepal.Width ~ Sepal.Length, group=Species, data=iris,
auto.key=list(space="right"),
jitter.x=TRUE, jitter.y=TRUE)
I'm working on trying to create a key for a heatmap, but as far as I know, I cannot use the existing tools for adding a legend since I've generated the colors myself (I manually turn a scaled variable into rgb values for a short rainbow ( [255,0,0] to [0,0,255] ).
Basically, all I want to do is use the rightmost 10th of the screen to create a rectangle with these 10 colors: "#0000FF", "#0072FF", "#00E3FF", "#00FFAA", "#00FF38", "#39FF00", "#AAFF00", "#FFE200", "#FF7100", "#FF0000"
with three numerical labels - at 0, max/2, and max
In essence, I want to manually produce an object that looks like a rudimentary heatmap color key.
As far as I know, split.screen can only split the screen in half, which isn't what I'm looking for. I want the graphic I already know how to produce to take up the leftmost 90% of the screen, and I want this colored rectangle to take up the other 10%.
Thanks.
EDIT: I greatly appreciate the advice about the best way to the the plot - that said, I still would like to know the best way to do the task originally asked - creating the legend by hand; I already am able to produce the exact heatmap graphic that I'm looking for - the false coloring wasn't the only problem with ggplot that I was having - it was just the final factor convincing me to switch. I need a non ggplot solution.
EDIT #2: This is close to the solution I am looking for, except this only goes up to 10 instead of accepting a maximum value as a parameter (I will be running this code on multiple data-sets, all with different maximum values - I want the legend to reflect this). Additionally, if I change the size of the graph, the key falls apart into disconnected squares.
Take a look at the layouts function (link). I think you want something like this:
layout(matrix(c(1,2), 1, 2, byrow = TRUE), widths=c(9,1))
## plot heatmap
## plot legend
I would also recommend the ggplot2 package and the geom_tile function which will take care of all of this for you.
Assuming your data is in a data frame with the x and y coordinates and heatmap value (e.g. gdat <- data.frame(x_coord=c(1,2,...), y_coord=c(1,1,...), val=c(6,2,...))) Then you should be able to produce your desired heat map plot with the following ggplot command:
ggplot(gdat) + geom_tile(aes(x=x_coord, y=y_coord, fill=val)) +
scale_fill_gradient(low="#0000FF", high="#FF0000")
To get your data into the following format you may want to look into the very useful reshape2 package.
Given a script no ggplot restriction on this answer here is how one could produce the plot with just base R.
colors <- c("#0000FF", "#0072FF", "#00E3FF", "#00FFAA", "#00FF38",
"#39FF00", "#AAFF00", "#FFE200", "#FF7100", "#FF0000")
layout(matrix(c(1,2), 1, 2, byrow = TRUE), widths=c(9,1))
plot(rnorm(20), rnorm(20), col=sample(colors, 20, replace=TRUE))
par(mar=c(0,0,0,0))
plot(x=rep(1,10), y=1:10, col=colors, pch=15, cex=7.1)
You may have to adjust the cex for your device.
I want to make a violin plot which is working fine. I have created the plot and added a title using the functions:
library(vioplot)
vioplot(x1, x2, x3, names=c("red", "green", "blue"), col="aliceblue") col="aliceblue")
title("Violin Plot")
But can't get the y or x axis titles which are the last things I need. I have tried.
ylab=("response")
ylab("response")
ylabel=("response")
ylabel("response")
All separately but it is not working. Do I have to include the y axis title in the main code for the plot?
Likewise I cannot label the X-axis ("colours").
Is this something which is beyond vioplot? and is there a way round it that is relatively basic?
Thanks
Ifvioplot (from an unnamed package) is a base or lattice graphics function, then you should set ylab="" in the call, and you can then use title(ylab="response", xlab="colours") to fill in with "response"/"colours" or whatever character values you desire. The title function is used (after a plot-like call) for several named locations on the abstract base plot layout: "main" for what most people would call "title", and/or "xlab" and "ylab" for the centered axis-descriptions (but not the tick labels) .
?title
This is probably a basic question. I’ve produced a plot that displays the home ranges for different lemurs. Great! Hard part done. But they are all lime green. How can I choose a different colour for each of my 5 ID's? It seems like is should be simple but I can’t see anything online. Would anyone be able to suggest something?
I’ve pasted my code below
dd <- read.csv(file.choose(), header = T)
xy <- dd[,c("X","Y")]
id <- dd[,"ID"]
hr<- mcp(xy,id,percent=95)
plot(hr,
main="95% Minimum Convex Polygon",
xlab="X Coordinate",
ylab="Y Coordinate")
Once i have 5 separate colors for my 5 ID's (frodo, bilbo, merry, pippin, sam) it would also be great to create a legend displaying the colors and the related ID. I was playing around with the following code
legend('topright', names(hr)[-1] ,
lty=1, col=c('red', 'blue', 'green',' brown'), bty='o', cex=1.5)
But that seems to just display a legend for the x,y coordinates not my ID's displayed in the plot. Can anyone tell me what i'm doing wrong?
Edit: I got it! The function "col=" doesnt work for polygons. Its "colpol=" Thanks for all the help
The hr object has a class of "area" and "data.frame". There is an area method for plot. It has a colpol argument. See ?plot.area when adehabitat is loaded:
plot(hr, colpol=c('red', 'blue', 'green',' brown') )
Originally it was not clear that you wanted to color the 4 (not 5) areas produced. I thought you wanted the points colored by group, which is what this produced.
If you know that ID is already a factor then the factor call is not needed. as.numeric applied to a factor turns it into an integer ranging from 1 to the number of levels, and that is being used as an index into that vector of 5 colors. If you want to see the names all of the 657 colors available, just type colors(). Refer to ?colors for additional links for managing color palettes.
As pointed out, we don't have the data or the mcp function to see what the hr object gets plotted as. If the plot method for that object is not assigning individual colors for the points, then do this instead:
points(xy[,1], xy[,2],
col = c("red", "green", "blue", "orange", "sandybrown")[as.numeric(factor(dd[,"ID"]))]
)
Is this what you are looking for
plot(hr$X,hr$Y,main="95% Minimum Convex Polygon",xlab="X Coordinate",
ylab="Y Coordinate",
col = rainbow(length(hr$ID))[rank(hr$ID)],
pch=c(1:25)[as.numeric(factor(hr$ID))])
legend('topleft', unique(unlist(as.character(factor(hr$ID)))) ,lty=1,
col=rainbow(length(hr$ID))[ unique(unlist(rank(hr$ID)))],
pch=c(1:25)[unique(unlist(as.numeric(factor(hr$ID))))],
bty='o', cex=1.5)