This code:
alTrack <- Gviz::AlignmentsTrack(
system.file(package = "Gviz", "extdata", "gapped.bam"),
isPaired = TRUE)
Gviz::plotTracks(
alTrack,
from = 3048500,
to = 3049000,
chromosome = "chr12")
Produces this plot:
Using the Gviz package. My problem is the empty space that's always appearing in the bottom of the picture. How can I remove a specific region of this plot / crop to only keep the region I need? If I could remove the lower 15% of a produced plot with an R function that would be great.
The specific region I want to not appear:
The max.height parameter will do it.
Already answered here:
https://support.bioconductor.org/p/81044/
Related
I am using the Treemap package in R to highlight the number of COVID outbreaks in different settings. I am making a number of different reports using R Markdown. Each one describes a different type of settings and I would like to highlight that setting in the treemap for each report, showing what proportion of total outbreaks occur in the setting in question. For example you I am currently working on the K-12 school report and would like to highlight the box representing that category in the figure.
I was previously using an exploded donut pie chart however there were two many subcategories and the graph became hard to read.
I am picturing a way to change the label or border on one specific box, ie. put a yellow border around the box or make the label yellow. I found a way to do both these things for all the boxes but not just one specific box. I made this image using the snipping tool to further illustrate what the desired outcome might look like. The code to generate the treemap can be found in the link below. It looks like this:
# library
library(treemap)
# Build Dataset
group <- c(rep("group-1",4),rep("group-2",2),rep("group-3",3))
subgroup <- paste("subgroup" , c(1,2,3,4,1,2,1,2,3), sep="-")
value <- c(13,5,22,12,11,7,3,1,23)
data <- data.frame(group,subgroup,value)
# treemap
treemap(data,
index=c("group","subgroup"),
vSize="value",
type="index"
)
This is the most straightforward information I can find about the package, this is where I took the sample image and code from: https://www.r-graph-gallery.com/236-custom-your-treemap.html
It looks like the treemap package doesn't have a built-in way to do this. But we can hack it by using the data frame returned by treemap() and adding a rectangle to the appropriate viewport.
# Plot the treemap and save the data used for plotting.
t = treemap(data,
index = c("group", "subgroup"),
vSize = "value",
type = "index"
)
# Add a rectangle around subgroup-2.
library(grid)
library(dplyr)
with(
# t$tm is a data frame with one row per rectangle. Filter to the group we
# want to highlight.
t$tm %>%
filter(group == "group-1",
subgroup == "subgroup-2"),
{
# Use grid.rect to add a rectangle on top of the treemap.
grid.rect(x = x0 + (w / 2),
y = y0 + (h / 2),
width = w,
height = h,
gp = gpar(col = "yellow", fill = NA, lwd = 4),
vp = "data")
}
)
I have a list of plots that I have assigned names to, and then converted to plot titles as suggested by https://stackoverflow.com/a/14790376/9335733. The titles happen to appear over the top x-axis title and so I attempt to move them as suggested here: https://stackoverflow.com/a/44618277/9335733. The overall code looks as follows:
lapply(names(Cast.files), function (x) plot(Cast.files[[x]],
main = x,
adj = 0, #adjust title to the farthest left
line =2.5 #adjust title up 2.5
)
)
It should be noted that plot is now converted from base R to the oce package for analyzing oceanographic data, but calls the same arguments from base R plot.
The problem becomes that in trying to move the title, the axis labels move as well and overlap. Any suggestions?
Edit: Here is what the image looks like before:
And after:
You might also want to look into the oma= argument in par(), which provides an "outer" margin which can be used to put a nice title. Something like:
library(oce)
data(ctd)
par(oma=c(0, 0, 1, 0))
plot(ctd)
title('Title', outer=TRUE)
This was solved by adding a title argument outside of the plot function as follows:
lapply(names(Cast.files), function (x) plot(Cast.files[[x]],
which = c("temperature", "salinity", "sigmaT","conductivity"),
Tlim = c(11,12),
Slim = c(29,32),
col = "red")
+ title(main = x, adj = 0.48, line = 3.5)#adding the titles at a specific location
)
This allowed for plots that looked like:
If you use the title function, rather than setting main within plot, it would allow you to change the line without affecting anything else in the plot.
I want to remove or rename the "top axis title" of the following plot based on the package plotmo. Here is a short reproducible example:
library(glmnet)
library(plotmo)
data(mtcars)
fit <- glmnet(x=as.matrix(mtcars[,-1]), y=as.matrix(mtcars[,1]))
plot_glmnet(fit)
Results in:
It looks like, that the plot is made by base plot functions. May someone knows a way to Change the top axis title or remove it
The only way I could achieve what you desire is by editing the source code.
plot_glmet.edited<- plot_glmnet ## copy the function
as.list(body(plot_glmet.edited)) ## print the lines of the function
At the moment the code will not print a label, replace NA with any character string that you want as a title
body(plot_glmet.edited)[[33]] <- substitute(
mtext(NA, side = 3, line = 1.5, cex = par("cex") * par("cex.lab")))
I'm still relatively inexperienced manipulating plots in R, and am in need of assistance. I ran a redundancy analysis in R using the rda() function, but now I need to simplify the figure to exclude unnecessary information. The code I'm currently using is:
abio1516<-read.csv("1516 descriptors.csv")
attach(abio1516)
bio1516<-read.csv("1516habund.csv")
attach(bio1516)
rda1516<-rda(bio1516[,2:18],abio1516[,2:6])
anova(rda1516)
RsquareAdj(rda1516)
summary(rda1516)
varpart(bio1516[,2:18],~Distance_to_source,~Depth, ~Veg._cover, ~Surface_area,data=abio1516)
plot(rda1516,bty="n",xaxt="n",yaxt="n",main="1516; P=, R^2=",
ylab="Driven by , Var explained=",xlab="Driven by , Var explained=")
The produced plot looks like this:
Please help me modify my code to: exclude the sites (sit#), all axes, and the internal dashed lines.
I'd also like to either expand the size of the field, or move the vector labels to all fit in the plotting field.
updated as per responses, working code below this point
plot(rda,bty="n",xaxt="n",yaxt="n",type="n",main="xxx",ylab="xxx",xlab="xxx
Overall best:xxx")
abline(h=0,v=0,col="white",lwd=3)
points(rda,display="species",col="blue")
points(rda,display="cn",col="black")
text(rda,display="cn",col="black")
Start by plotting the rda with type = "n" which generates an empty plot to which you can add the things you want. The dotted lines are hard coded into the plot.cca function, so you need either make your own version, or use abline to hide them (then use box to cover up the holes in the axes).
require(vegan)
data(dune, dune.env)
rda1516 <- rda(dune~., data = dune.env)
plot(rda1516, type = "n")
abline(h = 0, v = 0, col = "white", lwd = 3)
box()
points(rda1516, display = "species")
points(rda1516, display = "cn", col = "blue")
text(rda1516, display = "cn", col = "blue")
If the text labels are not in the correct position, you can use the argument pos to move them (make a vector as long as the number of arrows you have with the integers 1 - 4 to move the label down, left, up, or right. (there might be better solutions to this)
I am trying to plot FEVD (forecast error variance decomposition) for my VAR analysis. As you can see on the image, the legend screws up the graph and information. as this is an automatically created legend, I don’t know how to reposition it. I do not know much yet about plotting in R.
The only code i use to get this is :
library(vars)
var <- VAR(varTable2 , p=4 , type = "both")
plot(fevd(var, n.ahead = 10 ))
Thanks in advance
Legends do not resize well in R. You have to set your plotting window first and then chart your data.
Here's how to do it in Windows. win.graph opens a blank plotting window of the specified width. In Unix/Linux, you should look at X11() and in Mac, at quartz(). You might also consider shorter variable names.
library(vars)
data(Canada)
colnames(Canada) <-c("Long column name1","Long column name2","Long column name3","Long column name4")
var <- VAR(Canada , p=4 , type = "both")
win.graph(width=13,height=8)
plot(fevd(var, n.ahead = 10 ))