The following code does not display properly the error bars:
rf.imp<- read.csv("importances_byaggregations.csv",head=TRUE,sep=",") #Changes when handling the data
rf.imp$flux <- as.character(rf.imp$flux)
rf.imp$flux<-factor(rf.imp$flux,levels=unique(rf.imp$flux))
rf.imp$aggregation <- as.character(rf.imp$aggregation)
rf.imp$aggregation<-factor(rf.imp$aggregation,levels=unique(rf.imp$aggregation))
cbbPalette <- c("#F0E442", "#CC79A7","#E69F00","#56B4E9", "#009E73") # Mimicking Python colors
rf.imp$rel.influence<-rf.imp$rel.influence*100
rf.imp$SD<-rf.imp$SD*100
limits <- aes(ymax = rf.imp$rel.influence + rf.imp$SD, ymin=rf.imp$rel.influence - rf.imp$SD)
ggplot(rf.imp, aes(variable,rel.influence,fill=variable)) +
geom_bar(stat="identity",position="dodge") + scale_fill_manual(values=cbbPalette)+
theme_bw(base_size = 32, base_family = "Helvetica")+
xlab("")+
ylab("Variable importance (%)")+
facet_grid(aggregation~flux)+
geom_errorbar(limits, width=0.5)+
scale_y_continuous(limits=c(-10,90))+
theme(legend.position="none",
strip.text.x = element_blank(),
strip.text.y = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
strip.background = element_blank(),
panel.border = element_rect(colour = "black"),
panel.border = element_rect(colour = "black", fill=NA, size=1))
I would like to obtaine the following figure, but with the geom_facets swaped.
However, I get something like this:
Am I doing something wrong?
Thanks!
Your minimal example is a little too long for me to dig into, but I strongly suspect that your problem comes from using absolute (rf.imp$...) references in your error bar limits. If you use
geom_errorbar(aes(ymax=rel.influence+SD,
ymin=rel.influence-SD), width=0.5)
I think that will fix the problem.
Related
I'm trying to create a scatter graph of a linear model. I have successfully created the graph using ggPredict and plot but the axis is coming out light grey (barely visible) no matter what I put in to change it:
self_acc2 <- ggpredict(model1, "mean.self")
plot(self_acc2)
p.model7 <- plot(self_acc2)
self_acc <- p.model7 +
geom_point(data = dat_excluded, aes(x = mean.self, y = mean.acc),
alpha = 0.5, colour = "blue", shape = "circle") +
geom_line(size = 1) +
xlim(0, 9) +
ylim(0, 1) +
theme(
panel.grid.major = element_blank(),
panel.grid.minor= element_blank(),
panel.background = element_blank(),
axis.line = element_line(colour = "black")) +
xlab("Self-Rated Accuracy") +
ylab("Mean accuracy") +
ggtitle("Relationship Between Self-Rated Accuracy and Actual Accuracy of Health Understanding")
self_acc
I used:
theme(axis.line = element_line(colour = "black"))
but this didn't affect the colour
I also tried:
plot(self_acc, colors="bw")
but this didn't change anything.
I also need to put axis tick marks and nothing is working for that either.
(I've only been using R for a few months, sorry if this is really basic! I also don't know how to properly lay this question out so I hope this is ok)
You could use axis.line.x.bottom and axis.line.y in your theme. I used the mtcars dataset to make it reproducible:
library(ggeffects)
library(ggplot2)
model1 <- lm(mpg~hp, data = mtcars)
self_acc2 <- ggpredict(model1, "hp")
p.model7 <- plot(self_acc2)
p.model7 +
theme(
panel.grid.major = element_blank(),
panel.grid.minor= element_blank(),
panel.background = element_blank(),
axis.line.x.bottom = element_line(colour = "black"),
axis.line.y = element_line(colour = 'black'))
Created on 2023-01-14 with reprex v2.0.2
If you want to add tick marks you can use axis.ticks:
p.model7 <- plot(self_acc2)
p.model7 +
theme(
panel.grid.major = element_blank(),
panel.grid.minor= element_blank(),
panel.background = element_blank(),
axis.ticks = element_line(colour = "black"),
axis.line.x.bottom = element_line(colour = "black"),
axis.line.y = element_line(colour = 'black'))
Created on 2023-01-14 with reprex v2.0.2
I tried to plot a matrix using geom_tile. However, I noticed there are two strange blocks appear at the top and bottom of my plot. My initial guess was these are ticks element. I've tried to specify the theme parameters as far as I know but no luck.
Basically, I want to remove the two wired blocks that I marked in red arrow. The left plot is something that I desired except the white block. The right plot is I tuned the plot.background in theme to show you there are something I don't know occupies the area.
Image here
I also attached the minimal code that could reproduce the left plot:
test2 <- matrix(runif(100*100),nrow = 100)
testdf <- test2 %>% reshape2::melt()
testdf$Var2 <- factor(testdf$Var2,levels=(seq(max(testdf$Var2),1))) # you could ignore this line
testdf %>% ggplot() + geom_tile(aes(x=Var2,y=Var1,fill=log2(value+1))) +
scale_fill_gradientn(colors = c("#ffffff","#f9c979","#ec8121","#b80217","#2f0006")) +
theme(axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.title = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(colour = "black", fill=NA, size=1),
plot.background = element_blank()) + coord_equal()
These blocks are the result of ggplot2's default expansion of the scale. To get rid of these block set the expansion to zero via scale_y_continuous:
library(ggplot2)
library(reshape2)
test2 <- matrix(runif(100*100),nrow = 100)
testdf <- reshape2::melt(test2)
testdf$Var2 <- factor(testdf$Var2,levels=(seq(max(testdf$Var2),1))) # you could ignore this line
ggplot(testdf) +
geom_tile(aes(x=Var2,y=Var1,fill=log2(value+1))) +
scale_y_continuous(expand = c(0,0)) +
scale_fill_gradientn(colors = c("#ffffff","#f9c979","#ec8121","#b80217","#2f0006")) +
theme(axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.title = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(colour = "black", fill=NA, size=1),
plot.background = element_blank()) + coord_equal()
I am trying to create a graph of value ranges so that they can be compared to a unique range (represented by a gray rectangle in the graph). I got the graph to work just like I wanted to it but I cannot effectively change the line weight of the error bars that I am using to represent the value ranges. The code it below with example figures.
### Graph with default line weights
ggplot(data=droplevels(wght2[which(wght2$Zone!="Oahu"),]), aes(x=wght2$num[wght2$Zone!="Oahu"], y=(wght2[which(wght2$Zone!="Oahu"),4]+wght2[which(wght2$Zone!="Oahu"),4+3])/2,
group= wght2[which(wght2$Zone!="Oahu"),2], color= wght2[which(wght2$Zone!="Oahu"),2])) +
geom_errorbar(aes(ymin=wght2[which(wght2$Zone!="Oahu"),4], ymax=wght2[which(wght2$Zone!="Oahu"),4+3], width=0.3, color=wght2[which(wght2$Zone!="Oahu"),2])) +
geom_rect(ymin=wght2[8,4], ymax=wght2[8,4+3], xmin=0.5, xmax=6+0.5, fill="gray25", linetype=0, alpha=0.07)+
scale_color_manual(values=c("forestgreen","deepskyblue3","gold"))+
scale_x_continuous(labels=levels(wght2$Zone), breaks=c(1,2,3.5,5.5))+
labs(x="Zone",y=measure3[4]) +
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
legend.text = element_text(size = 16),
legend.title = element_text(size=16),
axis.text = element_text(size = 16,colour="black"),
axis.title = element_text(size = 18)) +
theme(legend.position="topright")
### My attempt to change line weights
ggplot(data=droplevels(wght2[which(wght2$Zone!="Oahu"),]), aes(x=wght2$num[wght2$Zone!="Oahu"], y=(wght2[which(wght2$Zone!="Oahu"),4]+wght2[which(wght2$Zone!="Oahu"),4+3])/2,
group= wght2[which(wght2$Zone!="Oahu"),2], color= wght2[which(wght2$Zone!="Oahu"),2])) +
geom_errorbar(aes(ymin=wght2[which(wght2$Zone!="Oahu"),4], ymax=wght2[which(wght2$Zone!="Oahu"),4+3], width=0.3, size=0.5, color=wght2[which(wght2$Zone!="Oahu"),2])) +
geom_rect(ymin=wght2[8,4], ymax=wght2[8,4+3], xmin=0.5, xmax=6+0.5, fill="gray25", linetype=0, alpha=0.07)+
scale_color_manual(values=c("forestgreen","deepskyblue3","gold"))+
scale_x_continuous(labels=levels(wght2$Zone), breaks=c(1,2,3.5,5.5))+
labs(x="Zone",y=measure3[4]) +
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
legend.text = element_text(size = 16),
legend.title = element_text(size=16),
axis.text = element_text(size = 16,colour="black"),
axis.title = element_text(size = 18)) +
theme(legend.position="topright")
As you can see from my code when I include the 'size' argument in the 'aes' function of geom_errorbar, the line weights become huge even though I set it at the default which is 0.5.
Any advice on how to change the line weights in geom_errorbar would be much appreciated. I know I could just draw each line in with geom_segment but feel like using geom_errorbar should work and want to know why it is not. Thanks!
I have effectively a very simple question.
I am using ggplot2 code to alter the font size of axis text and labels. However, wherever I position the command, none of the changes are visible on the axes. All other commands are working, so I am getting the impression that something is 'overriding' the theme(axis.text..., axis.title...) command.
ggplot(Cannock, aes(x=Capacity,color=CPType)) +
geom_histogram(fill="white",position="identity",binwidth=3,lwd=1) +
labs(title="Cannock Chase",x="Capacity", y = "Count") +
theme(axis.text=element_text(size=14), axis.title=element_text(size=16,face="bold")) +
facet_grid(CPType ~ .) +
geom_vline(data=mu1, aes(xintercept=grp.mean, color=CPType), linetype="dashed",size=1) +
theme_bw() +
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank()) +
theme(legend.position="none") +
theme(strip.text.y = element_text(size=8, fac[![enter image description here][1]][1]e="bold"), strip.background = element_rect(colour="white", fill="white")) +
coord_cartesian(xlim = c(0,100)) +
theme(strip.background = element_blank(), strip.text = element_blank())
Any pointers for this would be greatly appreciated. Many thanks!
I think it might be that you've called theme_bw() after you change your axis text formatting. Any formatting that you want to change from defaults needs to be changed after calling theme_bw. Additionally, just to be a little cleaner and tighter, you can combine all of your theme arguments into one group so that it's easier to keep track of what you're changing. Does the code below solve the problem?
You also specify strip.text and strip.background twice, with different settings, which is probably not what you want to do.
ggplot(Cannock, aes(x=Capacity,color=CPType)) +
geom_histogram(fill="white",position="identity",binwidth=3,lwd=1) +
labs(title="Cannock Chase",x="Capacity", y = "Count") +
facet_grid(CPType ~ .) +
geom_vline(data=mu1, aes(xintercept=grp.mean, color=CPType), linetype="dashed",size=1) +
theme_bw() +
coord_cartesian(xlim = c(0,100)) +
theme(axis.text=element_text(size=14),
axis.title=element_text(size=16,face="bold"),
axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
legend.position="none",
strip.text.y = element_text(size=8, face="bold"),
strip.text = element_blank(),
strip.background = element_rect(colour="white", fill="white"),
strip.background = element_blank())
I am struggling with ggplot to produce the legend of this figure. For now, I am only doing for one map, when it works I'l produce the four maps in the same plot.
I would like a legend like this: bottom, title in the center and above the scale, labels and colors, and omit the NA values.
Here is my code:
Reading the shapefile and installing a new variable
map_ev#data$id = rownames(map_ev#data)
map_ev.points = fortify(map_ev, region="id")
map_ev.df = join(map_ev.points, map_ev#data, by="id")
map_ev.df$median_norm = map_ev.df$median / map_ev.df$VOM
Vector with theme opts for ggplot
theme_opts <- list(theme(panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
axis.line = element_blank(),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
axis.ticks = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
plot.title = element_text(size=12, hjust=0.5),
legend.position = "bottom",
legend.title=element_blank()))
Installing the variable breaks
map_ev.df$median_norm <- cut(map_ev.df$median_norm, breaks=c(-200, -100, -50, -20, -5, 0, 5, 20, 50, 100, +200))
Checking the breaks
levels(map_ev.df$median_norm)
Colors to be used
color_map <- palette(c("#5b2e07", "#904d07", "#b98436", "#dfc27e", "#f6e8c3",
"#c9e9e4", "#84cdc4", "#3c958f", "#01675a", "#073a31"))
ggplot code
ggplot(map_ev.df) +
aes(long,lat,group=group,fill=median_norm, color=median_norm) +
geom_polygon() + geom_path(color="black") +
labs(title="Equivalent variation") + coord_equal() +
theme_opts
For now I am getting this figure:
Thanks all, I appreciate your help!
I just noticed you wanted manual colours for the fill. You can use:
myscale <- c("(-1,10]"="#BBDF27", "(10,20]"="#43BF71", "(20,30]"="#21908C", "(30,50]"="#35608D", "(50,101]"="#482576", "(101,300]"="#ffeeed")
combined with:
scale_fill_manual(values=myscale,na.value="#e0e0e0",name="",labels=c("<10","10 - 20","20 - 30","30 - 50", ">50","Estimate", "NA"))
where scale_fill manual replaces scale_fill_brewer in the other answer.
Just replace the colour and label values with your own. The values that need to go into myscale are shown when you plot your map without any labels. Good luck!
The reason you don't have a title, is because you never specified one, and if you did, you're deleting it again by writing legend.title=element_blank() in theme. Instead I rewrote it to specify the title should be centered. Using guides(colour = guide_legend(title.position = "top"),fill = guide_legend(title.position = "top",nrow=1,byrow=TRUE)) I set the position to "top" and made sure it will only be one row of legend items. (I left colour= here in case you do need it).
You also seem to want black borders, this means I deleted all colour= since that specifies the colour of the borders.
I've added a scale_fill_brewer, there are more color palettes available. Within this you can specify your legend title and the appearance of your legend labels. These need to be manually adjusted every time you change your input data, by the way.
I don't know how to remove the legend item for NA, sorry.
This is the total code I came up with:
ggplot(map_ev.df) +
aes(long,lat,group=group,fill=median_norm) +
scale_fill_brewer(palette="BrBG",name= "Title of legend",labels=c("-200 - -100","-100 - 50","-5 - 0","0 - 5", "label for NA"))+
geom_polygon() + geom_path(color="black") +
labs(title="Equivalent variation") + coord_equal() +
theme(panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
axis.line = element_blank(),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
axis.ticks = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
plot.title = element_text(size=12, hjust=0.5),
legend.position = "bottom",
legend.direction = "horizontal",
legend.title = element_text(hjust=0.5))+
guides(colour = guide_legend(title.position = "top"),fill = guide_legend(title.position = "top",nrow=1,byrow=TRUE))
Using some data of my own for the fill:
map