I am trying to create a polygon on one of my graphs I create in ggplot2 in order to denote a "compositional field". I understand that I should be using the geom_polygon function, but I was unable to successfully input this function. The code I have for my graph is below (less geom_polyon). I included a photo of what I am trying to do on my graph. Essentially, I want to create a polyogon between (x = 8, y = 0.8) and (x = 100, y = 2). Any help is greatly appreciate, thank you.
Image
[1]: https://i.stack.imgur.com/MR8pj.png
Graph script
ggplot(data = ZonesPd, aes(x = Pd_ppm, y = Cu.Pd)) +
geom_point(aes(color = Mineralized.Zone, size = Mineralized.Zone), alpha = 0.5) +
scale_x_log10(limit = c(1e-3, 1e3), expand = c(0, 0)) +
scale_y_log10(limit = c(1e2, 1e5), expand = c(0, 0)) +
scale_size_manual(values = c(0.5, 0.5, 3)) +
theme(panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.ticks.length = unit(-0.24, "cm"),
axis.text.x = element_text(size = 15, color = "black", margin = margin(0.5, 0.5, 0.5, 0.5,
"cm")),
axis.text.y = element_text(size = 15, color = "black", margin = margin(0.5, 0.5, 0.5, 0.5,
"cm")),
axis.title = element_text(size = 15),
aspect.ratio = 0.75,
legend.position = c(0.8, 0.15),
legend.text = element_text(size = 15),
legend.title = element_blank())
As suggested by r2evans in the comments, geom_rect is the way to go here:
library(ggplot2)
ZonesPd <- data.frame(Pd_ppm <- 10^rnorm(100), Cu.Pd <- 10^rnorm(100),
Mineralized.Zone=sample(gl(5,20)))
ggplot() +
geom_point(data = ZonesPd, aes(x = Pd_ppm, y = Cu.Pd, color = Mineralized.Zone, size = Mineralized.Zone), alpha = 0.5) +
scale_x_log10() + scale_y_log10() +
geom_rect(aes(xmin=8, xmax=100, ymin=0.8, ymax=8))
If you are happy with your plot and just want to add a rectangle with corners at (x = 8, y = 0.8) and (x = 100, y = 2), try adding:
+ geom_polygon(data = data.frame(x = c(8, 8, 100, 100), y = c(.8, 2, 2, .8)),
aes(x = x, y = y, alpha = 0.5))
Related
I have a stack of raster's and suppose to find the mean of it. I have done it. Now, I want to add polygon on the mean of raster image that I got. Then, I wants to save and make it colorful by using ggplot2 code. But I don't understand how to and where add polygon in ggplot2.
fs <- list.files(path="directory.tiff", pattern =
"tif$", full.names = TRUE)
s<- raster::stack(fs)
pg <- readOGR("parks.shp")
se1 <- calc(s, fun = mean)
plot(se1)
plot(pg, add= T )
They give me this attached below picture, Parks overlay on the mean of raster's. Its fine till now.
But when I used ggplot to change its color scheme. They gave me desired pattern what I want, but the problem is parks polygons doesn't overlay on the final picture (attached below after code what I get). So can anyone tell me where I need to change the code in ggplot to get park shp overlay on the picture 2.
conti_col_pal <- pnw_palette("Bay",10,type="continuous")
binary.cols <- c("1" = conti_col_pal[10], "0" = "white")
cv.df <- as.data.frame(rasterToPoints(se1))
##above I give the comand of se1 when I add pg here instead it give me error.
p_cv <- ggplot() +
coord_fixed() +
geom_raster(data = xy_FONDO, aes(lon, lat, fill = r)) +
scale_fill_gradient(low = "gray56", high = "gray56", na.value = NA, guide = FALSE) +
new_scale("fill") +
geom_raster(data = cv.df, aes(x, y, fill = layer))+
scale_fill_gradientn(colours = conti_col_pal,
breaks = seq(-1, 7, 2), limits = c(0, 10))+
annotate(geom = "text", x = lonmin+2, y = latmax-2, vjust = 1, hjust = 0,
label = "",
color = "black", angle = 0, size=4)+
scale_x_continuous(limits = c(lonmin, lonmax), expand = c(0, 0)) +
scale_y_continuous(limits = c(latmin, latmax), expand = c(0, 0))+
theme_bw(base_family="")+
theme(
plot.margin = margin(0, 0, 0, 0, "cm"),
#panel.background = element_rect(fill = col_pal_binary[1], colour = col_pal_binary[1], size
= 0.5, linetype = "solid"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank(),
axis.text.x=element_blank(),
axis.text.y=element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
legend.background = element_rect(fill=NA, size=0.3, linetype="solid", color=NA),
legend.position = c(0.8, 0.35),
legend.title= element_blank(),
legend.text = element_text(colour = "black", size = 12, angle = 0),
legend.direction = "vertical", ##vertical; horizontal
legend.title.align=0.5)+
guides(fill = guide_colorbar(## label.position = "bottom",
## title.position = "left",
label.vjust=0,
# draw border around the legend
frame.colour = "black",
barwidth = 1.5,
barheight = 8))
tiff(filename = "bay.tiff", res = 600,
width = 4080, height = 3200, compression = "lzw")
grid.arrange(p_cv,
ncol = 1)
dev.off()
After defining the raster "d.f" do same for pg but use function fortify to do and similarly after "geom_raster" do "geom_polygon" to introduce the polygon in ggplot.
I have a set of points in a scatter plot as below. I want to change the shape of one point or few points. I searched for this but could not find a way to do it.
I want to achieve like this
And like this
Code:
df <- data.frame(x = c(1,2,2,3,3.5,4,4.5,5,5.5,6,1.5,2,2,2,2,1.5,2.5,3,3,3,3,5.5,5,6,5.5,7)
,y = c(2,1,2,2,2,2,2,2,1.5,2,2.5,3,3.5,4,4.5,3.5,3.5,2,3,3.5,4,2.5,3,3,4,3.5))
library(ggplot2)
library(extrafont)
# helper dataframe for axis
df_arrow <- data.frame(x = c(0, 0),
y = c(0, 0),
xend = c(0, 8),
yend = c(8, 0))
ggplot(df,aes(x, y)) +
geom_point(colour = "blue", size = 5, shape = 3)+
scale_x_continuous(breaks = 1:7, expand = expansion(add = c(0, 1)))+
scale_y_continuous(breaks = 1:7, expand = expansion(add = c(0, 1)))+
coord_fixed(xlim = c(0, 7), ylim = c(0, 7), clip = "off")+
geom_segment(data = df_arrow, aes(x = x, xend = xend, y = y, yend = yend), size = 0.75, colour = "black",
arrow = arrow(angle = 20, length = unit(3, "mm"), ends = "last", type = "closed"), linejoin = "mitre") +
annotate("text", x = c(7.8, 0.3), y = c(0.3, 7.8), label = c("italic(x)", "italic(y)"), parse = TRUE, size = 6, family = "Times New Roman")+
labs(x = NULL,
y = NULL)+
theme_bw()+
theme(panel.grid.major = element_line(colour = "gray80"),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
axis.ticks.length = unit(1, "mm"),
text = element_text(size = 18, family = "Times New Roman"))
How is this?
Create a new column using dplyr::mutate, which is conditional upon the x-coordinates (for example, but it could be anything). Then, use this column within aes to control the shape size.
Also, you can use scale_shape_manual and scale_colour_manual to manually control the shape and colours. It's not clear to me what shape you want but you would just need to change the arguments in scale_shape_manual.
EDIT:
Since you specifically need a different symbol, then you need to use geom_text instead.
df %>%
dplyr::mutate(z = ifelse(x >= 5, "-", "+")) %>%
ggplot(aes(x, y)) +
geom_text(size = 12, aes(colour=z, label=z)) +
scale_x_continuous(breaks = 1:7, expand = expansion(add = c(0, 1)))+
scale_y_continuous(breaks = 1:7, expand = expansion(add = c(0, 1)))+
coord_fixed(xlim = c(0, 7), ylim = c(0, 7), clip = "off")+
geom_segment(data = df_arrow, aes(x = x, xend = xend, y = y, yend = yend), size = 0.75, colour = "black",
arrow = arrow(angle = 20, length = unit(3, "mm"), ends = "last", type = "closed"), linejoin = "mitre") +
annotate("text", x = c(7.8, 0.3), y = c(0.3, 7.8), label = c("italic(x)", "italic(y)"), parse = TRUE, size = 6, family = "Times New Roman")+
labs(x = NULL,
y = NULL)+
theme_bw()+
theme(panel.grid.major = element_line(colour = "gray80"),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
axis.ticks.length = unit(1, "mm"),
text = element_text(size = 18, family = "Times New Roman")) +
scale_shape_manual(values=c(8, 9)) +
scale_colour_manual(values = c('red', 'blue'))
I would like to create the plot below using ggplot.
Does anyone know of any geom that create the shaded region below the line chart?
Thank you
I think you're just looking for geom_area. However, I thought it might be a useful exercise to see how close we can get to the graph you are trying to produce, using only ggplot:
Pretty close. Here's the code that produced it:
Data
library(ggplot2)
library(lubridate)
# Data points estimated from the plot in the question:
points <- data.frame(x = seq(as.Date("2019-10-01"), length.out = 7, by = "month"),
y = c(2, 2.5, 3.8, 5.4, 6, 8.5, 6.2))
# Interpolate the measured points with a spline to produce a nice curve:
spline_df <- as.data.frame(spline(points$x, points$y, n = 200, method = "nat"))
spline_df$x <- as.Date(spline_df$x, origin = as.Date("1970-01-01"))
spline_df <- spline_df[2:199, ]
# A data frame to produce a gradient effect over the filled area:
grad_df <- data.frame(yintercept = seq(0, 8, length.out = 200),
alpha = seq(0.3, 0, length.out = 200))
Labelling functions
# Turns dates into a format matching the question's x axis
xlabeller <- function(d) paste(toupper(month.abb[month(d)]), year(d), sep = "\n")
# Format the numbers as per the y axis on the OP's graph
ylabeller <- function(d) ifelse(nchar(d) == 1 & d != 0, paste0("0", d), d)
Plot
ggplot(points, aes(x, y)) +
geom_area(data = spline_df, fill = "#80C020", alpha = 0.35) +
geom_hline(data = grad_df, aes(yintercept = yintercept, alpha = alpha),
size = 2.5, colour = "white") +
geom_line(data = spline_df, colour = "#80C020", size = 1.2) +
geom_point(shape = 16, size = 4.5, colour = "#80C020") +
geom_point(shape = 16, size = 2.5, colour = "white") +
geom_hline(aes(yintercept = 2), alpha = 0.02) +
theme_bw() +
theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
panel.grid.minor.y = element_blank(),
panel.border = element_blank(),
axis.line.x = element_line(),
text = element_text(size = 15),
plot.margin = margin(unit(c(20, 20, 20, 20), "pt")),
axis.ticks = element_blank(),
axis.text.y = element_text(margin = margin(0,15,0,0, unit = "pt"))) +
scale_alpha_identity() + labs(x="",y="") +
scale_y_continuous(limits = c(0, 10), breaks = 0:5 * 2, expand = c(0, 0),
labels = ylabeller) +
scale_x_date(breaks = "months", expand = c(0.02, 0), labels = xlabeller)
I am trying to generate a barplot with dual Y-axis and error bars. I have successfully generated a plot with error bars for one variable but I don't know how to add error bars for another one. My code looks like this. Thanks.
library(ggplot2)
#Data generation
Year <- c(2014, 2015, 2016)
Response <- c(1000, 1100, 1200)
Rate <- c(0.75, 0.42, 0.80)
sd1<- c(75, 100, 180)
sd2<- c(75, 100, 180)
df <- data.frame(Year, Response, Rate,sd1,sd2)
df
# The errorbars overlapped, so use position_dodge to move them horizontally
pd <- position_dodge(0.7) # move them .05 to the left and right
png("test.png", units="in", family="Times", width=2, height=2.5, res=300) #pointsize is font size| increase image size to see the key
ggplot(df) +
geom_bar(aes(x=Year, y=Response),stat="identity", fill="tan1", colour="black")+
geom_errorbar(aes(x=Year, y=Response, ymin=Response-sd1, ymax=Response+sd1),
width=.2, # Width of the error bars
position=pd)+
geom_line(aes(x=Year, y=Rate*max(df$Response)),stat="identity",color = 'red', size = 2)+
geom_point(aes(x=Year, y=Rate*max(df$Response)),stat="identity",color = 'black',size = 3)+
scale_y_continuous(name = "Left Y axis", expand=c(0,0),limits = c(0, 1500),breaks = seq(0, 1500, by=500),sec.axis = sec_axis(~./max(df$Response),name = "Right Y axis"))+
theme(
axis.title.y = element_text(color = "black"),
axis.title.y.right = element_text(color = "blue"))+
theme(
axis.text=element_text(size=6, color = "black",family="Times"),
axis.title=element_text(size=7,face="bold", color = "black"),
plot.title = element_text(color="black", size=5, face="bold.italic",hjust = 0.5,margin=margin(b = 5, unit = "pt")))+
theme(axis.text.x = element_text(angle = 360, hjust = 0.5, vjust = 1.2,color = "black" ))+
theme(axis.line = element_line(size = 0.2, color = "black"),axis.ticks = element_line(colour = "black", size = 0.2))+
theme(axis.ticks.length = unit(0.04, "cm"))+
theme(plot.margin=unit(c(1,0.1,0.1,0.4),"mm"))+
theme(axis.title.y = element_text(margin = margin(t = 0, r = 4, b = 0, l = 0)))+
theme(axis.title.x = element_text(margin = margin(t = 0, r = 4, b = 2, l = 0)))+
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank())+
ggtitle("SRG3")+
theme(legend.position="top")+
theme( legend.text=element_text(size=4),
#legend.justification=c(2.5,1),
legend.key = element_rect(size = 1.5),
legend.key.size = unit(0.3, 'lines'),
legend.position=c(0.79, .8), #width and height
legend.direction = "horizontal",
legend.title=element_blank())
dev.off()
and my plot is as follows:
A suggestion for future questions: your example is far from being a minimal reproducible example. All the visuals an the annotations are not related to your problem but render the code overly complex which makes it harder for others to work with it.
The following would be sufficient:
ggplot(df) +
geom_bar(aes(x = Year, y = Response),
stat = "identity", fill = "tan1",
colour = "black") +
geom_errorbar(aes(x = Year, ymin = Response - sd1, ymax = Response + sd1),
width = .2,
position = pd) +
geom_line(aes(x = Year, y = Rate * max(df$Response)),
color = 'red', size = 2) +
geom_point(aes(x = Year, y = Rate * max(df$Response)),
color = 'black', size = 3)
(Notice that I've removed stat = "identity" in all geom_s because this is set by default. Furthermore, y is not a valid aestetic for geom_errorbar() so I omitted that, too.)
Assuming that the additional variable you would like to plot error bars for is Rate * max(df$Response)) and that the relevant standard deviation is sd2, you may simply append
+ geom_errorbar(aes(x = Year, ymin = Rate * max(df$Response) - sd2,
ymax = Rate * max(df$Response) + sd2),
colour = "green",
width = .2)
to the code chunk above. This yields the output below.
For a final article submission I have been asked to update my figures so that they meet the following specifications:
axis lines are 0.25 mm
axis lines all around with ticks facing in
data lines are 0.5 mm
font is 10pt
figures should be 80 or 169 mm wide
must be 300 dpi
What I've tried:
library(ggplot2)
library(cowplot)
theme_set(theme_bw())
x <- rnorm(100)
mydata <- data.frame(x = x,
y = x^2 + runif(100),
z = rep(letters[1:4], 25))
p <- ggplot(data = mydata, aes(x, y)) +
geom_point(aes(color = z)) +
geom_smooth(color = 'black', se = FALSE, size = 0.5) +
theme(text = element_text(family = 'Times', size = 10, color = 'black'),
axis.ticks.length = unit(-0.1, 'cm'),
axis.text.x = element_text(margin = margin(t = 4, unit = 'mm')),
axis.text.y = element_text(margin = margin(r = 4, unit = 'mm')),
panel.grid = element_blank(),
axis.line = element_line(size = 0.25),
legend.position = c(0.5, 0.75))
p
ggsave(plot = p,
filename = 'myplot.png',
width = 80, height = 50, dpi = 300, units = 'mm')
p2 <- cowplot::plot_grid(plotlist = list(p, p, p, p), nrow = 1)
ggsave(plot = p2,
filename = 'mymultipleplot.png',
width = 169, height = 50, dpi = 300, units = 'mm')
Which returns the following two plots:
I can figure out how to handle some of the issues here (e.g. legend positions), but am having difficulty with the following:
How can I get ticks around top and right axes?
How can I get the sizes correct ...
These look much bigger than 10 pt. (download them or open in new window to see unscaled version)
The sizes are not maintained in the two figures despite being specified in the theme (font, line).
I don't know how to confirm that the lines are the correct size (in points or mm)... does ggsave do its own scaling?
update For my present task I exported as svg files and edited them in Inkscape. It took a few hours but was easier than getting ggplot to contort to the specifications.
But, it would be helpful to know for the future how to do this programmatically within ggplot2.
Answer to question:
1) as Henrik told in comments:
For question 1 (How can I get ticks around top and right axes?), see the new sec.axis argument in scale_ in ggplot 2.2.0. Try e.g. ggplot(mpg, aes(displ, hwy)) + geom_point() + scale_x_continuous(sec.axis = dup_axis()) + scale_y_continuous(sec.axis = dup_axis())
2) the problem here is that you have the same resolution with different sizes. Since the height of the two figures is the same, you can fix this problem scaling the font size by hand multiplying the font-size with the ratio of the width: e.g.
theme(text = element_text(family = 'Times', size = 10*(80/169), color = 'black')
The whole code should look like this:
library(ggplot2)
library(cowplot)
theme_set(theme_bw())
x <- rnorm(100)
mydata <- data.frame(x = x,
y = x^2 + runif(100),
z = rep(letters[1:4], 25))
p1 <- ggplot(data = mydata, aes(x, y)) +
geom_point(aes(color = z)) + scale_x_continuous(sec.axis = dup_axis()) +
scale_y_continuous(sec.axis = dup_axis()) +
geom_smooth(color = 'black', se = FALSE, size = 0.5) +
theme(text = element_text(family = 'Times', size = 10*(80/169), color = 'black'),
axis.ticks.length = unit(-0.1, 'cm'),
axis.text.x = element_text(margin = margin(t = 4, unit = 'mm')),
axis.text.y = element_text(margin = margin(r = 4, unit = 'mm')),
panel.grid = element_blank(),
axis.line = element_line(size = 0.25),
legend.position = c(0.5, 0.75))
p2 <- ggplot(data = mydata, aes(x, y)) +
geom_point(aes(color = z)) + scale_x_continuous(sec.axis = dup_axis()) +
scale_y_continuous(sec.axis = dup_axis()) +
geom_smooth(color = 'black', se = FALSE, size = 0.5) +
theme(text = element_text(family = 'Times', size = 10, color = 'black'),
axis.ticks.length = unit(-0.1, 'cm'),
axis.text.x = element_text(margin = margin(t = 4, unit = 'mm')),
axis.text.y = element_text(margin = margin(r = 4, unit = 'mm')),
panel.grid = element_blank(),
axis.line = element_line(size = 0.25),
legend.position = c(0.5, 0.75))
p1
ggsave(plot = p1,
filename = 'myplot.png',
width = 80, height = 50, dpi = 300, units = 'mm')
p2multi <- cowplot::plot_grid(plotlist = list(p2, p2, p2, p2), nrow = 1)
ggsave(plot = p2multi ,
filename = 'mymultipleplot.png',
width = 169, height = 50, dpi = 300, units = 'mm')