I posted my original question yesterday which got solved perfectly here
Original post
I made a few addition to my code
library(lubridate)
library(ggplot2)
library(grid)
### Set up dummy data.
dayVec <- seq(ymd('2016-01-01'), ymd('2016-01-10'), by = '1 day')
dayCount <- length(dayVec)
dayValVec1 <- c(0,-0.22,0.15,0.3,0.4,0.10,0.17,0.22,0.50,0.89)
dayValVec2 <- c(0,0.2,-0.17,0.6,0.16,0.41,0.55,0.80,0.90,1.00)
dayValVec3 <- dayValVec2
dayDF <- data.frame(Date = rep(dayVec, 3),
DataType = factor(c(rep('A', dayCount), rep('B', dayCount), rep('C', dayCount))),
Value = c(dayValVec1, dayValVec2, dayValVec3))
ggplot(dayDF, aes(Date, Value, colour = DataType)) +
theme_bw() +
ggtitle("Cumulative Returns \n") +
scale_color_manual("",values = c("#033563", "#E1E2D2", "#4C633C"),
labels = c("Portfolio ", "Index ", "In-Sample ")) +
geom_rect(aes(xmin = ymd('2016-01-01'),
xmax = ymd('2016-01-06'),
ymin = -Inf,
ymax = Inf
), fill = "#E1E2D2", alpha = 0.03, colour = "#E1E2D2") +
geom_line(size = 2) +
scale_x_datetime(labels = date_format('%b-%d'),
breaks = date_breaks('1 day'),
expand = c(0,0)) +
scale_y_continuous( expand = c(0,0), labels = percent) +
theme(axis.text.x = element_text(angle = 90),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major.x = element_blank(),
axis.line = element_line(size = 1),
axis.ticks = element_line(size = 1),
axis.text = element_text(size = 20, colour = "#033563"),
axis.title.x = element_text(hjust = 2),
plot.title = element_text(size = 40, face = "bold", colour = "#033563"),
legend.position = 'bottom',
legend.text = element_text(colour = "#033563", size = 20),
legend.key = element_blank()
)
which produces this output
The only thing that I still cannot get working is the position of the x axis. I want the x axis to be at y = 0 but still keep the x axis labels under the chart, exactly as in the excel version of it. I know the data sets are not the same but I didn't have the original data at hand so I produced some dummy data. Hope this was worth a new question, thanks.
> grid.ls(grid.force())
GRID.gTableParent.12660
background.1-5-7-1
spacer.4-3-4-3
panel.3-4-3-4
grill.gTree.12619
panel.background.rect.12613
panel.grid.minor.y.zeroGrob.12614
panel.grid.minor.x.zeroGrob.12615
panel.grid.major.y.polyline.12617
panel.grid.major.x.zeroGrob.12618
geom_rect.rect.12607
GRID.polyline.12608
panel.border.rect.12610
axis-l.3-3-3-3
axis.line.y.polyline.12631
axis
axis-b.4-4-4-4
axis.line.x.polyline.12624
axis
xlab.5-4-5-4
ylab.3-2-3-2
guide-box.6-4-6-4
title.2-4-2-4
> grid.gget("axis.1-1-1-1", grep=T)
NULL
ggplot2 doesn't make this easy. Below is one-way to approach this interactively. Basically, you just grab the relevant part of the plot (the axis line and ticks) and reposition them.
If p is your plot
p
grid.force()
# grab the relevant parts - have a look at grid.ls()
tck <- grid.gget("axis.1-1-1-1", grep=T)[[2]] # tick marks
ax <- grid.gget("axis.line.x", grep=T) # x-axis line
# add them to the plot, this time suppressing the x-axis at its default position
p + lapply(list(ax, tck), annotation_custom, ymax=0) +
theme(axis.line.x=element_blank(),
axis.ticks.x=element_blank())
Which produces
A quick note: the more recent versions of ggplot2 have the design decision to not show the axis. Also changes to axis.line are not automatically passed down to the x and y axis. Therefore, I tweaked your theme to define axis.line.x and axis.line.y separately.
That siad, perhaps its easier (and more robust??) to use geom_hline as suggested in the comments, and geom_segment for the ticks.
Related
This heatmap has a grid builtin, which I am failing to find the way to customize.
I want to preserve horizontal lines in the grid, if possible increase thickness, and disable vertical lines. Each row should look as a continuous time-serie where data is present and blank where it is not.
Either adding vertical/horizontal lines on-top would possibly cover some data, because of that grid lines, or controlled gaps between tiny rectangles, is preferable.
Alternativelly, geom_raster doesn't shows any grid at all. With which I would need to add the horizontal lines of the grid.
I tried changing linetype, the geom_tile argument, which does seem to change the type or allow to fully disable it with linetype=0, fully disabling the grid, but it wouldn't allow to preserve horizontal grid-lines. I didn't saw any changes by modifying the size argument.
This is the code generating the plot as above:
ggplot( DF, aes( x=rows, y=name, fill = value) ) +
#geom_raster( ) +
geom_tile( colour = 'white' ) +
scale_fill_gradient(low="steelblue", high="black",
na.value = "white")+
theme_minimal() +
theme(
legend.position = "none",
plot.margin=margin(grid::unit(0, "cm")),
#line = element_blank(),
#panel.grid = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.spacing = element_blank(),
#panel.grid = element_line(color="black"),
#panel.grid.minor = element_blank(),
plot.caption = element_text(hjust=0, size=8, face = "italic"),
plot.subtitle = element_text(hjust=0, size=8),
plot.title = element_text(hjust=0, size=12, face="bold")) +
labs( x = "", y = "",
#caption= "FUENTE: propia",
fill = "Legend Title",
#subtitle = "Spaces without any data (missing, filtered, etc)",
title = "Time GAPs"
)
I tried to attach DF %>% dput but I get Body is limited to 30000 characters; you entered 203304. If anyone is familiar with a similar Dataset, please advise.
Additionally,
There are 2 gaps at left&right of the plot area, one is seen inbetween the y-axis, and at the right you can see the X-axis outbounding, and are not controlled by a plot.margin argument.
I would want to set the grid to a thicker line when month changes.
The following data set has the same names and essential structure as your own, and will suffice for an example:
set.seed(1)
DF <- data.frame(
name = rep(replicate(35, paste0(sample(0:9, 10, T), collapse = "")), 100),
value = runif(3500),
rows = rep(1:100, each = 35)
)
Let us recreate your plot with your own code, using the geom_raster version:
library(ggplot2)
p <- ggplot( DF, aes( x=rows, y=name, fill = value) ) +
geom_raster( ) +
scale_fill_gradient(low="steelblue", high="black",
na.value = "white") +
theme_minimal() +
theme(
legend.position = "none",
plot.margin=margin(grid::unit(0, "cm")),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.spacing = element_blank(),
plot.caption = element_text(hjust=0, size=8, face = "italic"),
plot.subtitle = element_text(hjust=0, size=8),
plot.title = element_text(hjust=0, size=12, face="bold")) +
labs( x = "", y = "", fill = "Legend Title", title = "Time GAPs")
p
The key here is to realize that discrete axes are "actually" numeric axes "under the hood", with the discrete ticks being placed at integer values, and factor level names being substituted for those integers on the axis. That means we can draw separating white lines using geom_hline, with values at 0.5, 1.5, 2.5, etc:
p + geom_hline(yintercept = 0.5 + 0:35, colour = "white", size = 1.5)
To change the thickness of the lines, simply change the size parameter.
Created on 2022-08-01 by the reprex package (v2.0.1)
Hello I am ploting a graph which will have the legend,width of legend items not same can any one help me to resolve my problem
data file
< https://drive.google.com/file/d/1EKhRwup3vUC3KVFOOh4XtKERIr8FQj3x/view?usp=sharing>
code I have used
df=read.table("test.txt",sep='\t', header=TRUE)
df = data.frame(df)
nCol <- 15
myCol <- viridis(n = nCol)
myCol
ggplot(df, aes(log(data1), log(data2),color=data3),cex=1.9)+
geom_point() +
scale_colour_stepsn(colours = c(myCol),breaks = seq(0,100,by=10))+
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black"))+
theme(text = element_text(size = 12, face="bold"),
legend.text = element_text(size = 7, face="bold"), legend.position="top",
legend.key.size = unit(10, "mm"),
legend.key.width=unit(10, "mm"))
at the end of legend 90-100 width is high compare to others
There are a couple of asides before addressing your main concern:
You can simplify your code by using scale_color_binned(type = "viridis"), which gives the same result as creating a vector of
viridis colors and interpolating them as you are doing, with the added advantage that you don't need to load the viridis library.
You can use log scales on the x and y axis without having to transform your
data, by using scale_x_log10() and scale_y_log10()
You can simplify your theme call by first calling theme_classic(), which gets rid of the need to specify all those element_blank() components.
For the specific problem that you encountered though, the reason for the appearance is that breaks are for the "internal" breaks of the binned scale. The outer edges of your scale are not breaks, but limits. By default, limits are not shown on binned scales, but you can turn them on using show.limits = TRUE after setting the limits to the desired value of c(0, 100)
So your above code can be rewritten as:
df <- read.table("test.txt", sep = "\t", header = TRUE)
ggplot(df, aes(log(data1), log(data2), color = data3), cex = 1.9) +
geom_point() +
scale_colour_binned(type = "viridis",
breaks = 1:9 * 10,
limits = c(0, 100),
show.limits = TRUE,
labels = function(x) round(x)) +
theme_classic() +
theme(text = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 7, face = "bold"),
legend.position = "top",
legend.key.size = unit(10, "mm"))
I am wondering why the text is trending higher in the plots... it won't stay put with the facet_wrap or facet_grid. In a more complex dataset plot, the text is illegible because of the overlap.
Below is data and code to reproduce the plot and issue. Adding geom="text" to stat_fit_glance, results in Error: Discrete value supplied to continuous scale .
library(ggpmisc)
library(ggplot2)
DF <- data.frame(Site = rep(LETTERS[20:24], each = 4),
Region = rep(LETTERS[14:18], each = 4),
time = rep(LETTERS[1:10], each = 10),
group = rep(LETTERS[1:4], each = 10),
value1 = runif(n = 1000, min = 10, max = 15),
value2 = runif(n = 1000, min = 100, max = 150))
DF$time <- as.numeric(DF$time)
formula1 <- y~x
plot1 <- ggplot(data=DF,
aes(x=time, y= value2,group=Site)) +
geom_point(col="gray", alpha=0.5) +
geom_line(aes(group=Site),col="gray", alpha=0.5) +
geom_smooth(se=F, col="darkorange", alpha=0.8, fill="orange",
method="lm",formula=formula1) +
theme_bw() +
theme(strip.text.x = element_text(size=10),
strip.text.y = element_text(size=10, face="bold", angle=0),
strip.background = element_rect(colour="black", fill="gray90"),
axis.text.x = element_text(size=10), # remove x-axis text
axis.text.y = element_text(size=10), # remove y-axis text
axis.ticks = element_blank(), # remove axis ticks
axis.title.x = element_text(size=18), # remove x-axis labels
axis.title.y = element_text(size=25), # remove y-axis labels
panel.background = element_blank(),
panel.grid.major = element_blank(), #remove major-grid labels
panel.grid.minor = element_blank(), #remove minor-grid labels
plot.background = element_blank()) +
labs(y="", x="Year", title = "")+ facet_wrap(~group)
plot1 + stat_fit_glance(method = "lm", label.x="right", label.y="bottom",
method.args = list(formula = formula1),
aes(label = sprintf('R^2~"="~%.3f~~italic(p)~"="~%.2f',
stat(..r.squared..),stat(..p.value..))),
parse = TRUE)
When the position of the labels is set automatically, the npcy position is increased for each level in the grouping variable. You map Site to the group aesthetic, as Site has 5 levels unevenly appearing in different facets, the rather crude algorithm in 'ggpmisc' positions the labels unevenly: the five rows correspond one to each of the five Sites. I have changed the mapping to use colour so that this becomes more obvious. I have also deleted all code that is irrelevant to this question.
plot1 <- ggplot(data=DF,
aes(x=time, y= value2, color=Site)) +
geom_smooth(se=F, alpha=0.8,
method="lm",formula=formula1) +
facet_wrap(~group)
plot1 +
stat_fit_glance(method = "lm", label.x="right", label.y="bottom",
method.args = list(formula = formula1),
aes(label = sprintf('R^2~"="~%.3f~~italic(p)~"="~%.2f',
stat(..r.squared..),stat(..p.value..))),
parse = TRUE) +
expand_limits(y = 110)
To use fixed positions one can pass the npcy coordinates if using the default "geom_text_npcy()" or passing data coordinates and using "geom_text()". One position corresponds to each level of the grouping factor Site. If the vector is shorter, it is recycled. Of course to fit more labels you can reduce the size of the text and add space by expanding the plotting area. In any case, in practice, you will need to indicate in a way or another which estimates correspond to which line.
plot1 +
stat_fit_glance(method = "lm", label.x="right", label.y= c(0.01, 0.06, 0.11, 0.01, 0.06),
method.args = list(formula = formula1),
aes(label = sprintf('R^2~"="~%.3f~~italic(p)~"="~%.2f',
stat(..r.squared..),stat(..p.value..))),
parse = TRUE, size = 2.5) +
expand_limits(y = 110)
Note: Error: Discrete value supplied to continuous scale when attempting to use
geom_text() is a bug in 'ggpmisc' that I fixed some days ago, but has not made it yet to CRAN (future version 0.3.3).
I am wondering if there is any way to get a manual right-side y-axis label when there is no scale, only facet headings.
Here's an example
library(dplyr)
library(Hmisc)
# Plot power vs. n for various odds ratios (base prob.=.1)
(n <- seq(10, 1000, by=10)) # candidate sample sizes
(OR <- as.numeric(sort(c(seq(1/0.90,1/0.13,length.out = 9),2.9)))) # candidate odds ratios, spanning the 95% CI centered around an odds ratio of 2.9
alpha <- c(.001, .01, .05)
# put all of these into a dataset and calculate power
powerDF <- data.frame(expand.grid(OR, n, alpha)) %>%
rename(OR = Var1, num = Var2, alph = Var3) %>%
arrange(OR) %>%
mutate(power = as.numeric(bpower(p1=.29, odds.ratio=OR, n=num, alpha = alph))) %>%
transform(OR = factor(format(round(OR,2),nsmall=2)))
# now plot
pPower <- ggplot(powerDF, aes(x = num, y = power, colour = factor(OR))) +
geom_line() +
facet_grid(factor(alph)~.) +
labs(x = "sample size") +
scale_colour_discrete(name = "Odds Ratio") +
scale_x_continuous(breaks = seq(0,1000,100)) +
scale_y_continuous(breaks = seq(0,1,.1)) +
theme_light() +
theme(axis.title.x = element_text(size = 12, face = "bold"),
axis.title.y = element_text(size = 12, face = "bold"),
axis.text = element_text(size = 11),
panel.grid.minor = element_blank(),
panel.grid.major.y = element_line(colour = "gray95"),
panel.grid.major.x = element_line(colour = "gray95"),
strip.text = element_text(colour = 'black', face = 'bold', size = 12),
legend.text = element_text(size = 12),
legend.title = element_text(size = 12, face = "bold"))
(Please forgive the cluttered axes labels, I had to reduce the size of the image to allow it to be uploaded).
I was wondering if there was any way to have an axis label saying 'significance level' down the right hand side of the graph?
Adding the following to scale_y_continuous seems one way to go (although a bunch of warnings)
sec.axis = sec_axis(trans=I, breaks=NULL, name="Significance")
Alternatively, you can add an additional strip that spans all the panels:
library(grid)
library(gtable)
g <- ggplotGrob(pPower)
rect <- grobTree(rectGrob(gp = gpar(fill = "grey70", col="grey70")),
textGrob("Significance", rot=-90, gp = gpar(col="black")))
g <- gtable_add_cols(g, g$widths[6], 6)
g <- gtable_add_grob(g, rect, l=7, t=7, b=11)
grid.newpage() ; grid.draw(g)
I have been trying to shift my legend title across to be centered over the legend contents using the guide function. I've been trying to use the following code:
guides(colour=guide_legend(title.hjust = 20))
I thought of trying to make a reproducable example, but I think the reason it's not working has something to do with the above line not matching the rest of my code specifically. So here is the rest of the code I'm using in my plot:
NH4.cum <- ggplot(data=NH4_by_Date, aes(x=date, y=avg.NH4, group = CO2, colour=CO2)) +
geom_line(aes(linetype=CO2), size=1) + #line options
geom_point(size=3) + #point symbol sizes
#scale_shape_manual(values = c(1, 16)) + #manually choose symbols
theme_bw()+
theme(axis.text.x=element_text(colour="white"), #change x axis labels to white.
axis.title=element_text(size=12),
axis.title.x = element_text(color="white"), #Change x axis label colour to white
panel.border = element_blank(), #remove box boarder
axis.line.x = element_line(color="black", size = 0.5), #add x axis line
axis.line.y = element_line(color="black", size = 0.5), #add y axis line
legend.key = element_blank(), #remove grey box from around legend
legend.position = c(0.9, 0.6))+ #change legend position
geom_vline(xintercept=c(1.4,7.5), linetype="dotted", color="black")+ #put in dotted lines for season boundaries
scale_color_manual(values = c("#FF6600", "green4", "#0099FF"),
name=expression(CO[2]~concentration~(ppm))) + #manually define line colour
scale_linetype_manual(guide="none", values=c("solid", "solid", "solid")) + #manually define line types
scale_shape_manual(values = c(16, 16, 16)) + #manually choose symbols
guides(colour=guide_legend(title.hjust = 20))+
scale_y_continuous(expand = c(0, 0), limits = c(0,2200), breaks=seq(0,2200,200))+ #change x axis to intercept y axis at 0
xlab("Date")+
ylab(expression(Membrane~available~NH[4]^{" +"}~-N~(~mu~g~resin^{-1}~14~day^{-1})))+
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
geom_errorbar(aes(ymin = avg.NH4 - se.NH4, #set y error bars
ymax = avg.NH4 + se.NH4),
width=0.1)
I have tried doing the following instead with no luck:
guides(fill=guide_legend(title.hjust=20)
I have also adjusted the hjust value from values between -2 to 20 just to see if that made a difference but it didn't.
I'll try to attach a picture of the graph so far so you can see what I'm talking about.
I've looked through all the questions I can on stack overflow and to the best of my knowledge this is not a duplicate as it's specific to a coding error of my own somewhere.
Thank-you in advance!!
The obvious approach e.g.
theme(legend.title = element_text(hjust = .5))
didn't work for me. I wonder if it is related to this open issue in ggplot2. In any case, one manual approach would be to remove the legend title, and position a new one manually:
ggplot(mtcars, aes(x = wt, y = mpg, colour = factor(cyl))) +
geom_point() +
stat_smooth(se = FALSE) +
theme_bw() +
theme(legend.position = c(.85, .6),
legend.title = element_blank(),
legend.background = element_rect(fill = alpha("white", 0)),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
annotate("text", x = 5, y = 27, size = 3,
label = "CO[2]~concentration~(ppm)", parse = TRUE)
Output: