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I have written following code for comparing between to different variables over a period. The code works fine but only problem is when i output the file as "jpeg" the lines are not smooth and my arrow is not as smooth as i like it to be in other words the graph feels very low quality. But when i output it as "pdf" i get smooth lines and graph is of higher quality. But pdf files are high in file size and i need to insert these graphs in word file. I find it relatively easy to append jpeg into the word file. So is it possible to improve image quality while being in jpeg format. I tried using res argument in jpeg() but it doesnot output the graph as it is displayed in the rstudio.
I will appreciate the help. Thanks!
code:
library(shape)
library(Hmisc)
### samples ######
xaxs = seq(1,30,length=30)
precip = sample(200:800, 30)
ero = sample(0:10, 30, replace = T)
#########
svpth = getwd()
nm = "try.jpeg"
jpeg(paste0(svpth,"/",nm), width=950 , height =760, quality = 200, pointsize =15)
par(mar= c(5,4,2,4), oma=c(1,1,1,1))
plot(xaxs,precip, type = "p", pch=15, col="green", ylim = c(200,1000),
xlab = "Year" , ylab = "", cex.main=1.5, cex.axis=1.5, cex.lab=1.5)
lines(xaxs, precip,lty =1, col="green")
# xtick<-seq(0,30, by=1)
# axis(side = 1, at=xtick, labels = FALSE )
minor.tick(nx=5, ny=2, tick.ratio=0.5, x.args = list(), y.args = list())
mtext("Depth (mm)", side = 2, line = 2.7, cex = 1.5)
par(new=T)
plot(xaxs, (ero * 10), ylim = c(0,max(pretty(range((ero * 10))))+20), type = "p", pch=20, cex=1.5, col="red", axes = F, xlab = "", ylab = "")
lines(xaxs, (ero * 10),lty =2, col="red")
axis(side = 4, at=pretty(range((ero * 10))), cex.axis = 1.5)
# mtext("Erosion (t/ha/yr)", side = 4, line = 2.2, cex = 1.5)
mtext(expression(paste("Erosion (t ", ha^-1, yr^-1, ")")), side = 4, line = 2.7, cex = 1.5)
legend("topleft", legend = c("Precipitation","Erosion"), lty = c(1,2), pch = c(15,20), col = c("green","red"), cex = 1.6, bty = "n")
####arrow
Arrows(7, 85, 11, 90,lwd= 1.1)
Arrows(26, 85, 21, 90, lwd= 1.1)
txt = "High erosion rates in \nwheat-planting years"
xt = 16
yt = 85
text(xt, yt, labels = txt, family="serif", cex = 1.23)
sw = strwidth(txt)+1.4
sh = strheight(txt) +6
frsz = 0.38
rect(xt - sw/2 - frsz, yt - sh/2 - frsz, xt + sw/2 + frsz, yt + sh/2 + frsz-1)
# legend(15,80, legend = c("High erosion rates in \nwheat-planting years\n"),
# xjust = 0.5, yjust = 0.5)
dev.off()
It didn't use base R, but this makes an svg, which is smaller than a jpeg and will create some beautiful images. MS Word has no problems with svg, either.
The svg-- 18 kb; the jpeg-- 592 kb for the same image.
Use if it works, if not, well, perhaps someone else could use it? This won't show in the plot pane in RStudio, it will show in the viewer pane.
After the code, I have an image of saving the plot in the viewer pane in RStudio.
library(plotly)
df = data.frame("Year" = xaxs, "Depth" = precip, "Erosion" = ero *10)
p = plot_ly(df) %>%
add_trace(x = ~Year, y = ~Depth,
type = 'scatter', mode = 'lines', # to have both the points and lines use 'lines+markers'
name = "Depth",
line = list(shape = "spline", # smooth the curves in the lines (not that effective with lines+markers)
color = "green")) %>%
add_trace(x = ~Year, y = ~Erosion,
mode = 'lines',
name = "Erosion",
yaxis = "y2", # second y axis
line = list(dash = 'dash', # dash the lines
shape = "spline", # smooth the curves in the lines
color = "red")) %>% # without "lines+markers" spline will smooth out the points of the line
add_annotations(inherit = F, # add the arrows at the top of the plot
x = list(12, 18), # this is plot coordinates
y = list(800, 800),
ax = list(-60, 60), # this is pixels
ay = list(10, 10),
showarrow = T,
text = "") %>%
add_annotations(inherit = F, # add the textbox at the top of the plot
x = 15, y = 800,
ax = 0, ay = 0,
showarrow = F,
bordercolor = 'black',
text = "High erosion rates in\nwheat-planting years") %>%
layout(yaxis2 = list(overlaying = "y", side = "right", # add labels
title = paste0("Erosion (t ",
"ha<sup>-1</sup>",
"yr<sup>-1</sup>",
")")),
yaxis = list(title = "Depth (mm)"),
legend = list(x = .1, y = 1000),
margin = list(r = 80)) # right margin space for label
To save it, add the functionality. The icons at the top of the plot in the image at the end won't show until you hover over them. I think you may find that if you use this, the height/width specifications you have aren't the best fit anymore.
(p <- p %>% config( # save the plot; add a save function to the plot
toImageButtonOptions = list(
format = "svg",
filename = "try",
width = 950,
height = 760)) # end config
) # end () for print simo object assignment
The plot. The width and height in this image are 950 x 550.
I've produced a simple line plot using base R and want to add data labels to the point. Any idea how to do this in an automated way? Picture of graph produced here
plot(grant$year, grant$grantee, type = "o", xlab = "Year", ylab = "Number of Grantees", pch = 16, col = "dark blue", lwd = 3, cex = 2)
I estimated your data from the linked picture. By adding text(grant$year, grant$grantee, labels = grant$grantee, pos = 3) after your plot gives us labels. pos = 3 puts the labels above the data points.
year <- c(2015,2016,2017,2018,2019,2020)
grantee <- c(50,55,51,30,52,83)
grant <- data.frame(year, grantee)
plot(grant$year, grant$grantee, type = "o", xlab = "Year", ylab = "Number of Grantees", pch = 16, col = "dark blue", lwd = 3, cex = 2)
text(grant$year, grant$grantee, labels = grant$grantee, pos = 3)
I create a data frame with four different rows. Every row has decreasing numbers. But I have some problems with the plot in the picture:
Everything is correct with the plot except that the grey bars are the wrong way round. Actually they would have to rise.
This is the syntax:
plot(z_RMSE_MAE$max_diff, z_RMSE_MAE$z_images_left, col.lab="black",yaxt='n',type = "o", xlab = "max Differenz", ylab ="", main ="",col = "red")
axis(4, col = "red")
par(new = T)
barplot(z_RMSE_MAE$z_MAE, type= "h", col = "grey",xlab ="", ylab = "",space = 0.8, density = 40, decreasing ="FALSE")
mtext(side = 2, line = 3, col = "grey" ,'MAE')
mtext(side = 4, line = 3, col = "red" ,'images left')
axis(side = 2 )
Can someone help me?
I have data from several sources describing an y value in a 360 degrees space but I cannot plot them together with a fitted spline on a single polar plot.
Here's some simulated data:
# Data for test
set.seed(35)
sim1 <- cbind(rnorm(6,0),seq(0,359,359/5))
sim2 <- cbind(rnorm(9,0),seq(0,359,359/8))
sim3 <- cbind(rnorm(7,0),seq(0,359,359/6))
If not doing a polar plot my procedure would be as follows:
# Create spline for points
total <- rbind(sim1,sim2,sim3)
fit= smooth.spline(total[,2],total[,1], cv=T)
# Classic solution if not polar plot
plot(sim1[,2],sim1[,1],ylim = c(-3,4), col = "darkgrey")
lines(sim1[,2],sim1[,1], pch=2, col = "darkgrey")
points(sim2[,2],sim2[,1], pch=2, col = "darkgrey")
lines(sim2[,2],sim2[,1], pch=2, col = "darkgrey")
points(sim3[,2],sim3[,1], pch=2, col = "darkgrey")
lines(sim3[,2],sim3[,1], pch=2, col = "darkgrey")
lines(fit, , col = "red")
Which would give me this kind of figure:
Plot
But trying to plot it in a polar plot. I cannot get further than plotting each individually:
# Plot
library(plotrix)
polar.plot(sim1[,1],sim1[,2],lwd=3,line.col="red", radial.lim=c(-3,3),clockwise=TRUE,rp.type = "s")
polar.plot(sim2[,1],sim2[,2],lwd=3,line.col="blue", radial.lim=c(-3,3),clockwise=TRUE,rp.type = "s")
polar.plot(sim3[,1],sim3[,2],lwd=3,line.col="darkgrey", radial.lim=c(-3,3),clockwise=TRUE,rp.type = "s")
Poor plot but 360
I have also tried using ggplot2 as well as plotly but nothing yielded what I was hoping for.
Use the add parameter to add lines. Perhaps something like this?
polar.plot(sim1[,1], sim1[,2], lwd=1, line.col = "grey20", radial.lim = c(-3,3),
clockwise = TRUE, rp.type = "p")
polar.plot(sim2[,1], sim2[,2], lwd=1, line.col = "grey20", radial.lim = c(-3,3),
clockwise = TRUE, rp.type = "p", add = TRUE)
polar.plot(sim3[,1], sim3[,2], lwd=1, line.col = "grey20", radial.lim = c(-3,3),
clockwise = TRUE, rp.type = "p", add = TRUE)
polar.plot(fit$y, fit$x, lwd=2, line.col = "firebrick", radial.lim = c(-3,3),
clockwise = TRUE, rp.type = "p", add = TRUE)
GGplot alternative:
library(ggplot2,ggthemes)
# Data for test
set.seed(35)
sim1 <- cbind(rnorm(6,0),seq(0,359,359/5))
sim2 <- cbind(rnorm(9,0),seq(0,359,359/8))
sim3 <- cbind(rnorm(7,0),seq(0,359,359/6))
# Create spline for points
total <- rbind(sim1,sim2,sim3)
colnames(total)=c('Col1','Col2')
total=as.data.frame(total)
MyNames=c(rep('sim1',nrow(sim1)),rep('sim2',nrow(sim2)),rep('sim3',nrow(sim3)))
total=cbind(MyNames,total)
Radial=ggplot(total)+
theme_light()+
geom_line(aes(x=Col2,y=Col1,group=MyNames,colour=MyNames),alpha=0.4)+
geom_point(aes(x=Col2,y=Col1,group=MyNames,colour=MyNames))+
geom_line(aes(x=Col2,y=Col1),stat='smooth', method = "loess", span=0.5, alpha=0.4, size=1.2)+
scale_x_continuous(breaks=seq(0,360,by=60),expand=c(0,0),lim=c(0,360))+
coord_polar(theta='x',start=0)+
ggtitle('Sim')+
theme(axis.text=element_text(size=14),axis.title=element_text(size=16,face="bold"),legend.text=element_text(size=14),legend.title=element_text(size=14),title=element_text(size=16,face="bold"),plot.title = element_text(hjust = 0.5))
Radial
I am using a function which plots two graphs on the same picture. I want to add threshold line to the first graph and a different threshold on the second graph. I am using abline() function to do so. chr6 comes with a library as an example.
install.packages("GenWin")
library(GenWin)
chrom_num = 6
jpeg(filename = paste(chrom_num, ".jpg", sep=""), width = 1200, height = 800)
chr = splineAnalyze(chr6$Fst, chr6$Position, plotRaw = 1, plotWindows = 1, method = 4)
abline(0.3, 0, col = "green")
abline(6, 0, col = "green")
Both threshold lines show up on the second graph. How to prevent this? In other word is there a way to direct to which graph I am adding something?
If you want to add something, I think it would be better to make graphs by yourself from the analyzed data, chr (almost all code is picked out from splineAnalyze). This approach would enable you to customize the graph.
analyzed_data <- chr # All you need to do is changing these lines and data and col names of 1st plot()).
smoothness <- 100 # default value
jpeg(filename = paste("file_name", ".jpg", sep=""), width = 1200, height = 800)
par(mfrow = c(2,1))
# 1st graph
plot(Fst ~ Position, chr6, xlab = "Position (bp)", ylab = "Raw values")
with(analyzed_data,
lines(x = seq(0, max(rawSpline$x), by = smoothness),
y = predict(rawSpline, seq(0, max(rawSpline$x), by = smoothness)), col = "red")
)
abline(0.3, 0, col = "green")
# 2nd graph
with(analyzed_data,
plot(x = (windowData$WindowStop - windowData$WindowStart)/2 + windowData$WindowStart,
y = windowData$Wstat, xlab = "Position (bp)", ylab = "Spline Wstat", pch = 19)
)
abline(6, 0, col = "green")
dev.off()
Of course, you can do it using splineAnalyze(..., plotRaw = 1, plotWindows = 1, ...) and adding the lines.
jpeg(filename = paste("file_name2", ".jpg", sep=""), width = 1200, height = 800)
chr = splineAnalyze(chr6$Fst, chr6$Position, plotRaw = 1, plotWindows = 1, method = 4)
abline(6, 0, col = "green") # draw on 2nd panel
layout(matrix(c(2,1), ncol = 1)) # refocus 1st panel
par(new = T)
plot(Fst ~ Position, chr6, ann = F, type = "n", axes = F) # reproduce the coordinates
abline(0.3, 0, col = "green") # draw on 1st panel
dev.off()