I have this code. Basically, when mousing over the ggplotly plot in the value=50, I have two labels overlapping each other so basically I cannot see the West label, only the South.
How can I prevent that from happening? What am I doing wrong? I would like to see both labels separated when mousing over.
library(ggplot2)
library(ggplotly)
data <- data.frame(
name=c( "A" ),
value=c( 30,40,50,50),
location=c("North","East", "West","South")
)
pxp<- ggplot(data, aes(x=name, y=value, text=location)) + geom_boxplot() +geom_point() +
theme_bw() + theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))+
labs(y="Value")
ggplotly(pxp)
Thank you,
You can use jitter and give appropriate width and height to see the points separately. Then it displays the appropriate values when you hover. Try this
pxp<- ggplot(data, aes(x=name, y=value, text=location)) + geom_boxplot() + # geom_point(position=jitter, width=0.1) +
geom_jitter(alpha=0.6, width=0.02, height=0.1)+
theme_bw() + theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))+
labs(y="Value")
ggplotly(pxp)
Related
How to change the plot.background in a 'geom_rect()' + 'coord.polar()' in a Donut ggplot graph?
I dont know what I´m missing, but I´w working in html black background style and needing to set panel as well plot background to black, but the graph sides of my ggplot are white and I need to know which attribute or command I need to use to turn sides to black too.
Below my code:
my_df %>%
ggplot(aes(ymax=max, ymin=min, xmax=4, xmin=3,fill=ResultCode)) +
geom_rect() +
geom_label( x=3.5, aes(y=labelPosition, label=label), size=4, color="white") +
coord_polar(theta="y") +
xlim(c(2, 4)) +
theme_void() +
theme(legend.position="none",
plot.background=element_rect(fill = "black"),
panel.background = element_rect(fill = "black"),
panel.border = element_blank(),
legend.key = element_blank(),
axis.ticks = element_blank(),
axis.text.y = element_blank(),
panel.grid = element_blank())
Below the resulted graph (see the "white" sides at right and left I need to fill with black)
The problem here is that ggplot by default calls grid::grid.newpage before drawing. This creates a blank (white) screen. It will then set up a square viewport to fit your plotting window because you are using coord_polar. Once it has done this, it considers the square area to be "the" plotting window. In a sense then, ggplot has no knowledge or control over these white areas. No theme element can touch it.
The solution is to explicitly call grid.newpage yourself, draw a black background manually, and then explicitly print your ggplot using the parameter newpage = FALSE. You could alternatively set the grid gpar parameters so that the background is black by default, but this is likely to have undesired side effects later on.
Here's a reprex with some made-up data:
my_df <- data.frame(max = c(160, 320), min = c(0, 161),
ResultCode = c("A","B"),
labelPosition = c(80, 240), label = c("A", "B"))
p <- my_df %>%
ggplot(aes(ymax=max, ymin=min, xmax=4, xmin=3,fill=ResultCode)) +
geom_rect() +
geom_label( x=3.5, aes(y=labelPosition, label=label), size=4, color="white") +
coord_polar(theta="y") +
xlim(c(2, 4)) +
theme(legend.position="none",
plot.background = element_rect(fill = "black", color = "black"),
panel.background = element_rect(fill = "black", color = "black"),
plot.margin = margin(0,0,0,0),
panel.border = element_blank(),
legend.key = element_blank(),
axis.ticks = element_blank(),
axis.text.y = element_blank(),
panel.grid = element_blank())
grid::grid.newpage()
grid::grid.draw(grid::rectGrob(gp = grid::gpar(fill = "black")))
print(p, newpage = FALSE)
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 make a stacked and grouped barplot using the following datasets:
dfplot <- data.frame(organisms=c("M.musculus","D.melanogaster" ,"H.sapiens","O.sativa","S.pombe","C.familiaris",
"G.gallus","P.falciparum","A.thaliana","C.elegans","D.rerio","B.taurus","S.cerevisiae","R.norvegicus","C.intestinalis","B.subtilis","E.coli"),
KEGGv2=c(20,7,21,126,106,62,26,80,5,5,13,306,8,35,32,104,107),
KEGGv1=c(286,124,289,0,0,244,135,0,121,124,148,0,101,271,87,0,0),
Reactome=c(358,146,596,115,54,306,370,23,155,112,365,341,52,364,0,0,0))
# Melt the dataframe
melted <- melt(dfplot, "organisms")
# Reformat the data labels
melted$cat <- ''
melted[melted$variable == 'Reactome',]$cat <- "Reactome"
melted[melted$variable != 'Reactome',]$cat <- "KEGG"
ggplot(melted, aes(x=cat, y=value, fill=variable)) +
geom_bar(stat = 'identity', position = 'stack') +
facet_grid(~ organisms)+
scale_fill_manual(values=c("deepskyblue4", "lightblue1", "olivedrab2")) +
labs(y = "Number of Pathways") +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
legend.title=element_blank(),
strip.text.x = element_blank(),
strip.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
axis.line = element_line(colour = "black"))
And my output is the following one:
I used a facet_grid per organism because I wanted to have a mix between stack (for both KEGGv1 and KEGGv2) and then group it with the other group Reactome. However, when doing the melting, the x-axis will have two labels per facet_grid (KEGG and Reactome, which is the variable obtained from the melting [cat]). I did not want that label so I remove them.
What I am trying to do is to have the organism name per each of the groupings, so each of the 17 grouping bars will have the name of the corresponding organism**. Therefore, I am missing that, I have tried several ways but I cannot find the proper way of doing it.
Thanks in advance,
You can do two things to make this work:
Rotate the labels of the facet so that they plot at 90 degrees
Plot the facet labels beneath the graph using the switch = 'x' argument within facet_grid.
Here is the complete example:
ggplot(melted, aes(x=cat, y=value, fill=variable)) +
geom_bar(stat = 'identity', position = 'stack') +
facet_grid(~organisms, switch = 'x')+
scale_fill_manual(values=c("deepskyblue4", "lightblue1", "olivedrab2")) +
labs(y = "Number of Pathways") +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
legend.title=element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
axis.line.y = element_line(colour = "black"),
strip.text = element_text(angle = 90))
I left the default shaded background, but you can easily style as you prefer.
Aproach Two
You might want to consider rotating the plot. This requires you to flip the coordinates of the plot using coord_flip before the facet is called. As we are faceting in the other direction we change the facet argument to facet_grid(organisms~.). All other arguments which refer to x or y are swapped over:
ggplot(melted, aes(x=cat, y=value, fill=variable)) +
geom_bar(stat = 'identity', position = 'stack') +
coord_flip() +
facet_grid(organisms~., switch = 'y') +
scale_fill_manual(values=c("deepskyblue4", "lightblue1", "olivedrab2")) +
labs(y = "Number of Pathways") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
legend.title=element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
axis.line.x = element_line(colour = "black"),
strip.text.y = element_text(angle = 180))
First you can set the organism labels to be below the bars, rather than above. This is established by setting the switch argument of the facet_grid function to "x" (see code below). Secondly, you should then remove axis.title.x=element_blank() argument within your theme function call. The updated code is below. Hope this helps!
ggplot(melted, aes(x = cat, y = value, fill =variable)) +
geom_bar(stat = 'identity', position = 'stack') +facet_grid(~organisms, switch="x")+
scale_fill_manual(values=c("deepskyblue4","lightblue1","olivedrab2"))+
ylab("Number of pathways")+
theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank())+theme(legend.title=element_blank())+
theme(strip.background = element_blank())+theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),panel.background = element_blank(), axis.line = element_line(colour = "black"))
I am trying to add a panel border to my plot - but the border keeps falling somewhere below the x-axis. Does anyone have any suggestions to have the bottom line of the panel border fall directly on the x-axis.
f<- ggplot(nadph, aes(x = reorder(DGRP.Line, MEN), y = MEN)) +
geom_bar(stat = "identity") +
xlab("DGRP Line") + ylab ("MEN activity (standardized)") +
theme(axis.text.x=element_blank(),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.ticks.x = element_blank(),
panel.border = element_rect(color = "black", fill= NA, size=1))
I have a plot in ggplot:
ggplot(plot1,aes(x=c,y=value,colour=variable,linetype=variable,size=variable)) +
geom_line() +
scale_x_continuous(breaks=seq(1,10,1)) +
scale_y_continuous(breaks=seq(0,1, 0.1))+
scale_colour_manual(values=rep(c("blue3","red3"),each=9)) +
scale_linetype_manual(values = rep(c(3,1),each=9)) +
scale_size_manual(values = rep(c(0.6,0.3),each=9)) +
theme_bw(base_size=12, base_family="Helvetica") +
theme(axis.text=element_text(size=8),
axis.title=element_text(size=8),
text = element_text(size=14),
axis.line = element_line(size=0.25),
axis.ticks=element_line(size=0.25),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
legend.position="none" ,
legend.direction="vertical",
legend.title=element_blank(),
legend.text=element_text(size=8),
legend.background=element_blank(),
legend.key=element_blank())+labs(title='a',x='b', y='c' )+theme(plot.title=element_text(size=8))+theme(plot.margin=unit(c(0.1,0,0.1,0),"cm"))
I would like to disable:
the numbers on the y axis
the small lines indicating the position of the numbers
the label
Is this possible to do without affecting the x axis?
I think you can use this approach.
p1 + theme(axis.text.y=element_blank())+ylab("") + scale_y_discrete(breaks=NULL)
# p1 = your initial graph
# axis.text.y removes number
# ylab("") removes y label
# scale_y_discrete(breaks=NULL) removes the tick marks. Your x-axis will not be affected.
Good luck.
You can also do everything in the theme() part of your code. Just add the following code:
p1 + theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())