Rescale y axis ggplot (geom_bar) - r

This is should be very simple question!
I would like to make a barplot with errorbars and I'm using the following code:
ggplot(data = bars, aes(x=c("1","2","3"), y=V2, fill = names)) +
geom_bar(position=position_dodge(), stat="identity", alpha = 0.7) +
geom_errorbar(aes(ymin=V1, ymax=V3))+
theme(legend.position='none')+
coord_cartesian(ylim=c(0,10))
However, I have 2 problems:
1. I would like the bars to start at y = 0
2. I don't like the ticks in the y axis. I would like numbers with just one decimal and less ticks.
this is my actual plot: Bars with error bars

For the first problem (if I understand it correctly) you can use ylim
... + ylim(0.2, NA)
NA leaves the upper bound free.
For the second, I suggest to use pretty_breaks from scale
library(scales)
... + scale_y_continuous(breaks=pretty_breaks(n=5))

Related

Is it possible to make a column plot using ggplot in which the column fill is controlled by a third variable?

I have a data frame with three continuous variables (x,y,z). I want a column plot in which x defines the x-axis position of the columns, y defines the length of the columns, and the column colors (function of y) are defined by z. The test code below shows the set up.
`require(ggplot2)
require(viridis)
# Create a dummy data frame
x <- c(rep(0.0, 5),rep(0.5,10),rep(1.0,15))
y <- c(seq(0.0,-5,length.out=5),
seq(0.0,-10,length.out=10),
seq(0.0,-15,length.out=15))
z <- c(seq(10,0,length.out=5),
seq(8,0,length.out=10),
seq(6,0,length.out=15))
df <- data.frame(x=x, y=y, z=z)
pbase <- ggplot(df, aes(x=x, y=y, fill=z))
ptest <- pbase + geom_col(width=0.5, position="identity") +
scale_fill_viridis(option="turbo",
limits = c(0,10),
breaks=seq(0,10,2.5),
labels=c("0","2.5","5.0","7.5","10.0"))
print(ptest)`
The legend has the correct colors but the columns do not. Perhaps this is not the correct way to do this type of plot. I tried using geom_bar() which creates a bars with the correct colors but the y-values are incorrect.
It looks like you have 3 X values that each appear 5, 10, or 15 times. Do you want the bars to be overlaid on top of one another, as they are now? If you add an alpha = 0.5 to the geom_col call you'll see the overlapping bars.
Alternatively, you might use dodging to show the bars next to one another instead of on top of one another.
ggplot(df, aes(x=x, y=y, fill=z, group = z)) +
geom_col(width=0.5, position=position_dodge()) +
scale_fill_viridis_c(option="turbo", # added with ggplot 3.x in 2018
limits = c(0,10),
breaks=seq(0,10,2.5),
labels=c("0","2.5","5.0","7.5","10.0"))
Or you might plot the data in order of y so that the smaller bars appear on top, visibly:
ggplot(dplyr::arrange(df,y), aes(x=x, y=y, fill=z))+
geom_col(width=0.5, position="identity") +
scale_fill_viridis_c(option="turbo",
limits = c(0,10),
breaks=seq(0,10,2.5),
labels=c("0","2.5","5.0","7.5","10.0"))
I solved this by using geom_tile() in place of geom_col().

Ggplot2 Boxplot width setting changes x-axis

I have produced a boxplot with a continuous x-axis unsing geom_boxplot() in ggplot2. However, as there are many boxes they appear as skinny lines. Another stackoverflow chain (see here) suggested using the width= argument to make all the boxes the same width. However, when I use this argument it changes the x-axis and some of the boxes just disappear!
For example, take this example dataframe. I apologise for the number of observations this has but I think the quantity has to do with the problem as I couldn't reproduce it with a more simple boxplot:
Lat<- c(50.70228,50.70228,50.70228,51.82067,51.82067,51.82067,52.45893,52.45893,52.45893,52.76478,52.76478,52.76478,52.78354,52.78354,52.78354,53.56102,53.56102,53.56102,53.65364,53.65364,53.65364,53.63130,53.63130,53.63130,54.19035,54.19035,54.19035,54.25751,54.25751,54.25751,54.23526,54.23526,54.23526,54.62469,54.62469,54.62469,54.67831,54.67831,54.67831,54.67900,54.67900,54.67900,54.94908,54.94908,54.94908,55.19456,55.19456,55.19456,54.79198,54.79198,54.79198,55.34981,55.34981,55.34981,55.85655,55.85655,55.85655,56.06078,56.06078,56.06078,55.84553,55.84553,55.84553,56.00197,56.00197,56.00197,56.71842,56.71842,56.71842,57.00116,57.00116,57.00116,57.06942,57.06942,57.06942,57.26815,57.26815,57.26815,57.45532,57.45532,57.45532,57.88596,57.88596,57.88596,51.07711,51.07711,51.07711,51.07801,51.07621,51.11159,51.11159,51.11159,52.02484,52.02484,52.02484,52.02581,52.02581,52.02581,52.02685,52.02685,52.02685,52.05353,52.05353,52.05626,52.05353,52.05353,52.05353,52.05353,52.05353,52.05353,51.93541,51.93541,51.93541,51.93541,51.93541,51.93541,51.93541,51.93541,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.90810,52.90810,52.90810,52.90810,52.90810,52.90810,52.78968,52.78778,52.78968,52.78968,52.78881,52.78883,52.78883,52.78883,52.78970,52.78970,52.79506,52.79506,52.79506,53.77270,53.77276,53.77109,53.77109,53.77276,53.76845,53.76845,53.77109,53.76845,53.77109,53.87020,53.87020,53.87020,53.87103,53.88205,53.88205,53.88205,53.88205,53.87701,53.87701,53.87098,53.87098,53.87098,53.86932,53.86932,53.86932,56.51869,56.51869,56.51869,56.55870,56.55870,56.55870,56.55964,56.55964,56.55964,57.51056,57.49542,57.49542,57.50878,57.50878,57.50878,57.45201,57.45477,57.45192,57.45192,57.45192)
y <- c(33.45407,21.40954,27.73487,20.38318,26.65483,31.68201,23.95467,20.77363,32.94192,22.71228,25.78824,28.39449,35.60615,24.29325,22.95047,25.65343,30.23262,22.05534,37.20565,35.53812,38.20211,39.38034,35.16619,38.82336,29.72370,38.25754,26.51339,39.38283,29.57483,31.80111,24.52967,34.83037,21.75038,35.50868,39.41830,21.96971,22.82504,32.69746,35.10747,27.75669,34.96690,37.61921,37.17226,20.50448,39.26582,22.08668,28.41502,36.69530,23.69404,23.18052,33.27420,23.04157,33.17285,32.00579,21.83845,22.97143,32.27190,21.53771,38.65481,20.14341,33.62718,39.86755,39.77881,30.59810,27.65909,24.11646,34.56981,29.30249,34.99361,32.39553,28.90443,34.88775,22.77049,36.44468,30.64496,35.81501,31.77673,24.19058,39.36298,21.47219,23.02268,31.37647,27.28457,33.14749,23.20842,39.73427,39.81399,35.51515,24.55080,39.41190,29.59987,38.46791,20.94479,37.22109,26.36060,30.91641,39.25975,39.88288,22.59061,30.24439,21.66110,30.36878,28.76901,38.75561,33.80408,31.05842,26.18921,21.30804,35.02966,33.85981,30.84373,31.67341,35.07605,37.93820,31.30481,21.45117,37.13626,25.70964,25.64736,38.58381,31.24448,26.55902,23.90817,33.70300,26.48909,37.73200,32.52413,22.44440,28.19878,32.46415,25.13711,26.66075,28.16254,20.40673,39.89327,30.83327,32.40196,39.81218,39.80391,21.87316,34.95792,33.38958,38.18441,22.03114,35.64410,34.90643,24.23056,36.66581,29.35813,20.86880,30.02044,36.13727,24.65558,39.43175,29.00154,29.78185,22.89196,37.15204,35.88188,28.73920,28.04934,37.50701,30.36306,28.39842,35.20973,26.54260,29.57763,26.03163,26.90440,27.60110,25.80086,39.98019,21.59970,28.83825,32.01711,20.50812,38.43331,32.41898,27.68722,32.59905,24.18150,29.05701,22.38512,32.93342,37.66694,37.65391,34.19613,23.89985,36.90012,20.74244,27.08511,29.21433,35.83771,35.59557,33.74533,27.08854,38.38994)
V3 <-c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2)
df <- as.data.frame(cbind(Lat, y, as.factor(V3)))
head(df)
I plot it on a continuous x-axis as so:
df_plot <- ggplot(df, aes(x=Lat, y=y, group=Lat))+
geom_boxplot(aes(colour=as.factor(V3)))+
theme_classic()
df_plot
Which produces:
As you can see the boxes are represented as skinny lines.
Therefore I tried to use the width= argument as so:
df_plot2 <- ggplot(df, aes(x=Lat, y=y, group=Lat))+
geom_boxplot(aes(colour=as.factor(V3)), width=1)+
theme_classic()
df_plot2
The output is:
The main thing to notice here is that the x-axis range has suddenly changed! Some of the boxes are no longer plotted whilst others seem to be placed at different values of the x-axis.
The range of the x-axis should be:
range(df$Lat)
[1] 50.70228 57.88596
I am completley perplexed as to why the x-axis would change by simply adding the width= argument in geom_boxplot(). I therefore tried to force the limits of the x-axis scale as so:
df_plot3 <- ggplot(df, aes(x=Lat, y=y, group=Lat))+
geom_boxplot(aes(colour=as.factor(V3)), width=1)+
xlim(50,58)+
theme_classic()
df_plot3
ouput:
Please send help!
I think the strange behaviour comes from ggplot trying to automatically dodge your boxplots apart. By setting position = position_dodge(width = 0) the plot seems to be created as expected without changing the placement of boxes along the x-axis. (But gives a warning about overlapping x intervals)
Lat<- c(50.70228,50.70228,50.70228,51.82067,51.82067,51.82067,52.45893,52.45893,52.45893,52.76478,52.76478,52.76478,52.78354,52.78354,52.78354,53.56102,53.56102,53.56102,53.65364,53.65364,53.65364,53.63130,53.63130,53.63130,54.19035,54.19035,54.19035,54.25751,54.25751,54.25751,54.23526,54.23526,54.23526,54.62469,54.62469,54.62469,54.67831,54.67831,54.67831,54.67900,54.67900,54.67900,54.94908,54.94908,54.94908,55.19456,55.19456,55.19456,54.79198,54.79198,54.79198,55.34981,55.34981,55.34981,55.85655,55.85655,55.85655,56.06078,56.06078,56.06078,55.84553,55.84553,55.84553,56.00197,56.00197,56.00197,56.71842,56.71842,56.71842,57.00116,57.00116,57.00116,57.06942,57.06942,57.06942,57.26815,57.26815,57.26815,57.45532,57.45532,57.45532,57.88596,57.88596,57.88596,51.07711,51.07711,51.07711,51.07801,51.07621,51.11159,51.11159,51.11159,52.02484,52.02484,52.02484,52.02581,52.02581,52.02581,52.02685,52.02685,52.02685,52.05353,52.05353,52.05626,52.05353,52.05353,52.05353,52.05353,52.05353,52.05353,51.93541,51.93541,51.93541,51.93541,51.93541,51.93541,51.93541,51.93541,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.92425,52.90810,52.90810,52.90810,52.90810,52.90810,52.90810,52.78968,52.78778,52.78968,52.78968,52.78881,52.78883,52.78883,52.78883,52.78970,52.78970,52.79506,52.79506,52.79506,53.77270,53.77276,53.77109,53.77109,53.77276,53.76845,53.76845,53.77109,53.76845,53.77109,53.87020,53.87020,53.87020,53.87103,53.88205,53.88205,53.88205,53.88205,53.87701,53.87701,53.87098,53.87098,53.87098,53.86932,53.86932,53.86932,56.51869,56.51869,56.51869,56.55870,56.55870,56.55870,56.55964,56.55964,56.55964,57.51056,57.49542,57.49542,57.50878,57.50878,57.50878,57.45201,57.45477,57.45192,57.45192,57.45192)
y <- c(33.45407,21.40954,27.73487,20.38318,26.65483,31.68201,23.95467,20.77363,32.94192,22.71228,25.78824,28.39449,35.60615,24.29325,22.95047,25.65343,30.23262,22.05534,37.20565,35.53812,38.20211,39.38034,35.16619,38.82336,29.72370,38.25754,26.51339,39.38283,29.57483,31.80111,24.52967,34.83037,21.75038,35.50868,39.41830,21.96971,22.82504,32.69746,35.10747,27.75669,34.96690,37.61921,37.17226,20.50448,39.26582,22.08668,28.41502,36.69530,23.69404,23.18052,33.27420,23.04157,33.17285,32.00579,21.83845,22.97143,32.27190,21.53771,38.65481,20.14341,33.62718,39.86755,39.77881,30.59810,27.65909,24.11646,34.56981,29.30249,34.99361,32.39553,28.90443,34.88775,22.77049,36.44468,30.64496,35.81501,31.77673,24.19058,39.36298,21.47219,23.02268,31.37647,27.28457,33.14749,23.20842,39.73427,39.81399,35.51515,24.55080,39.41190,29.59987,38.46791,20.94479,37.22109,26.36060,30.91641,39.25975,39.88288,22.59061,30.24439,21.66110,30.36878,28.76901,38.75561,33.80408,31.05842,26.18921,21.30804,35.02966,33.85981,30.84373,31.67341,35.07605,37.93820,31.30481,21.45117,37.13626,25.70964,25.64736,38.58381,31.24448,26.55902,23.90817,33.70300,26.48909,37.73200,32.52413,22.44440,28.19878,32.46415,25.13711,26.66075,28.16254,20.40673,39.89327,30.83327,32.40196,39.81218,39.80391,21.87316,34.95792,33.38958,38.18441,22.03114,35.64410,34.90643,24.23056,36.66581,29.35813,20.86880,30.02044,36.13727,24.65558,39.43175,29.00154,29.78185,22.89196,37.15204,35.88188,28.73920,28.04934,37.50701,30.36306,28.39842,35.20973,26.54260,29.57763,26.03163,26.90440,27.60110,25.80086,39.98019,21.59970,28.83825,32.01711,20.50812,38.43331,32.41898,27.68722,32.59905,24.18150,29.05701,22.38512,32.93342,37.66694,37.65391,34.19613,23.89985,36.90012,20.74244,27.08511,29.21433,35.83771,35.59557,33.74533,27.08854,38.38994)
V3 <-c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2)
library(ggplot2)
df <- as.data.frame(cbind(Lat, y, as.factor(V3)))
df_plot <- ggplot(df) +
geom_boxplot(aes(colour=as.factor(V3), x=Lat, y=y, group=as.factor(Lat)),
position=position_dodge(width = 0),
width=1) +
theme_classic()

Realigning x-axis on geom_histogram in ggplot2

When creating a geom_histogram in ggplot, the bin labels appear directly underneath the bars. How can I make it so that they appear on either side of the bin, so that they describe the range of each bin (so that the bin that includes cases from 0 to 10 will appear between the 0 and 10 labels)?
I tried using
geom_histogram(position=position_nudge(5))
However, the histogram I'm using is stacked (to differentiate categories within each bin), and this effect is ruined when I add this position. Is there another way of doing it? Maybe moving the axis labels themselves instead of the bars?
Reproducible code:
dd<-data.frame(nums=c(1:20,15:30,40:55),cats=c(rep("a",20),rep("b",30),rep("c",2)))
ggplot(dd, aes(nums))+geom_histogram(aes(nums,fill=cats),dd,binwidth = 10)
results in this:
I want the bars to be shifted to the right by 5, so that the 0 aligns with the left-hand side of the histogram
You can try to define breaks and labels
n <- 10
ggplot(dd, aes(nums, fill=cats)) +
geom_histogram(binwidth = n, boundary = 0) +
scale_x_continuous(breaks = seq(0,55,n), labels = seq(0,55, n))
The following moves the labels of the axis. I wasn't sure how to move the ticks on the x axis so I removed them.
ggplot(dd, aes(nums))+geom_histogram(aes(nums),dd,binwidth = 10)+
theme(axis.text.x = element_text(hjust = 5),
axis.ticks.x = element_blank())

pie chart in ggplot text labelling horror

I can't resolve that strange situation. Somewhere I have error, or bug, but sitting over three halfs of an hour could not deal with it.
I have: sta_df
sta value
1 IN_LIQUIDATION 29
2 LIQUIDATED 47
3 OPERATING 435
4 TRANSFORMED 8
sp <- ggplot(sta_df, aes(x="", y=value, fill=sta)) +
geom_bar(width = 1, stat = "identity", color = "black") +
coord_polar("y") + scale_fill_brewer(palette="Pastel2") +
geom_text(aes(x = seq(1.2,1.4,,4), label = percent(value/sum(value))),
position = position_stack(vjust = 0.5), size=5)
and the plot have wrong direction of labelling.
Nevermind this strange font of a picture. I've tried to use many different functions instead of position_stack. For example:
geom_text(aes(x = rep(seq(0.9,1.4,,6),1), y = value/2 + c(0, cumsum(value)[-length(value)])
but it didn't help. This thread neither: wrong labeling in ggplot pie chart
When I wanted to reverse y=rev(value) the legend didn't correspond with data. Putting direction 1 or -1 doesn't do more than reversing all. Reversing values in geom_text gives Pac-Man-like chart. I've updated ggplot2.
Honestly, the problem is because chart starts to draw anti-clockwise although direction is set to clockwise and text numbers are in right direction. And reversing data in data.frame doesn't change anything in the whole plot. Sorry, I stuck, but feel the solution is right there.
The problem occurs when you assign different x-values to your labels in geom_label(). Why? Because you are relying on position_stack() to give you your y-values. But when the points no longer share the same x, then they don't get 'stacked' anymore. If you want to customize the x-values, you will need to compute your own y-values, as described here (Showing data values on stacked bar chart in ggplot2) and here (http://docs.ggplot2.org/current/geom_text.html) near bottom of the page. By the way, I did all my troubleshooting with coord_polar removed, just looking at the plain barplot version.
Anyway, here is a partial solution:
sta_df <- read.table(header=TRUE,
text=" sta value
IN_LIQUIDATION 29
LIQUIDATED 47
OPERATING 435
TRANSFORMED 8")
library(ggplot2)
library(scales)
sta_df$fraction = sta_df$value / sum(sta_df$value)
sp <- ggplot(sta_df, aes(x="", y=value, fill=sta)) +
geom_bar(width=1, stat="identity", color="black",) +
scale_fill_brewer(palette="Pastel2") +
coord_polar(theta="y") +
geom_text(aes(x=1.4, label=percent(fraction)),
position=position_stack(vjust=0.5), size=4)
ggsave("pie_chart.png", plot=sp, height=4, width=6, dpi=150)

Why doesn't geom_hline generate a legend in ggplot2?

I have some code that is plots a histogram of some values, along with a few horizontal lines to represent reference points to compare against. However, ggplot is not generating a legend for the lines.
library(ggplot2)
library(dplyr)
## Siumlate an equal mix of uniform and non-uniform observations on [0,1]
x <- data.frame(PValue=c(runif(500), rbeta(500, 0.25, 1)))
y <- c(Uniform=1, NullFraction=0.5) %>% data.frame(Line=names(.) %>% factor(levels=unique(.)), Intercept=.)
ggplot(x) +
aes(x=PValue, y=..density..) + geom_histogram(binwidth=0.02) +
geom_hline(aes(yintercept=Intercept, group=Line, color=Line, linetype=Line),
data=y, alpha=0.5)
I even tried reducing the problem to just plotting the lines:
ggplot(y) +
geom_hline(aes(yintercept=Intercept, color=Line)) + xlim(0,1)
and I still don't get a legend. Can anyone explain why my code isn't producing plots with legends?
By default show_guide = FALSE for geom_hline. If you turn this on then the legend will appear. Also, alpha needs to be inside of aes otherwise the colours of the lines will not be plotted properly (on the legend). The code looks like this:
ggplot(x) +
aes(x=PValue, y=..density..) + geom_histogram(binwidth=0.02) +
geom_hline(aes(yintercept=Intercept, colour=Line, linetype=Line, alpha=0.5),
data=y, show_guide=TRUE)
And output:

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