if I use ggplot on this dataframe
library(ggplot2)
date <- as.Date(c("2019-12-18",
"2019-12-19",
"2019-12-20",
"2019-12-23",
"2019-12-24",
"2019-12-26",
"2019-12-27",
"2019-12-30"))
measures <- c( 0.0000000000,
0.0012376239,
-0.0024768434,
0.0024768434,
0.0043196611,
0.0091939970,
-0.0006103144,
-0.0030571104)
theData <- data.frame(date, measures, I=measures<0)
ggplot(theData) + geom_point( aes(x=date, y=measures, col=as.factor(I), size=factor(I))) +
scale_size_discrete(range = c(0.8, 2), guide="none") +
scale_color_manual(values = c("grey80", "steelblue4"), breaks = c("TRUE"), labels = c("negative")) +
labs( col="") +
theme(legend.position = c(0.2, 0.8))
# )
the legend box keeps the space for the FALSE level in the variable I. I tried resizing the legend box with legend.margin, but with no success. If the background of the legend and of the plot are different, it looks quite ugly. Any suggestion?
The reason for the empty gap on the top of the legend was not a space left for the unused factor level "FALSE", but an empty line due to labs( col="").
The correct way to eliminate the legend title is legend.title = element_blank(). Further fine tuning for the label margins can be obtained through legend.margin.
My complete ggplot command is:
ggplot(theData) + geom_point( aes(x=date, y=measures, col=as.factor(I), size=factor(I))) +
scale_size_discrete(range = c(0.8, 2), guide="none") +
scale_color_manual(values = c("grey80", "steelblue4"), breaks = c("TRUE"), labels = c("negative")) +
theme(legend.position = c(0.2, 0.8), legend.title = element_blank(), legend.margin = margin(0, 0.3, 0.2, 0.2, "cm"))
Related
Consider the following example where a scatter is made and only the "significant" point are colored and labelled.
genes <- read.table("https://gist.githubusercontent.com/stephenturner/806e31fce55a8b7175af/raw/1a507c4c3f9f1baaa3a69187223ff3d3050628d4/results.txt", header = TRUE)
genes$Significant <- ifelse(genes$padj < 0.05, "FDR < 0.05", "Not Sig")
ggplot(genes, aes(x = log2FoldChange, y = -log10(pvalue))) +
geom_point(aes(color = Significant)) +
scale_color_manual(values = c("red", "grey")) +
theme_bw(base_size = 12) + theme(legend.position = "bottom") +
geom_text_repel(
data = subset(genes, padj < 0.05),
aes(label = Gene),
size = 5,
box.padding = unit(0.35, "lines"),
point.padding = unit(0.3, "lines")
)
It yields the following plot
Now imagine that the labels are actually acronyms and that they have a real full-length name (e.g., "DOK6" is the acronym for "Duo Ocarino Kayne 6"). Would it be possible to add a legend to the plot where the keys are the labels used on the plot, and the entries are the full-length name of the labels ?
First, I added Gene2 for another legend which only shows significant Gene.\
Next, Gene2 was added on the aes as a fill. (Only color would affect the color of points on geom_point).\
Finally, scale_fill_discrete was added for the second legend. All you need to do is just annotate the full-length name column at Full names here.
genes$Gene2 <-ifelse(genes$padj<0.05, genes$Gene, NA)
ggplot(genes, aes(x = log2FoldChange, y = -log10(pvalue),
fill=Gene2)) +
geom_point(aes(color = Significant)) +
scale_color_manual(values = c("red", "grey")) +
theme_bw(base_size = 12) + theme(legend.position = "bottom") +
geom_text_repel(
data = subset(genes, padj < 0.05),
aes(label = Gene),
size = 5,
box.padding = unit(0.35, "lines"),
point.padding = unit(0.3, "lines")
) +
scale_fill_discrete(labels=paste0(genes$Gene,': ',' Full names here'),
name='Significant genes') +
theme(legend.position = 'right')
Output
I'm trying to add set of markers with text above the top of a faceted chart to indicate certain points of interest in the value of x. Its important that they appear in the right position left to right (as per the main scale), including when the overall ggplot changes size.
Something like this...
However, I'm struggling to:
place it in the right vertical position (above the facets). In my
reprex below (a simplified version of the original), I tried using a
value of the factor (Merc450 SLC), but this causes issues such as adding that to
every facet including when it is not part of that facet and doesn't
actually go high enough. I also tried converting the factor to a number using as.integer, but this causes every facet to include all factor values, when they obviously shouldn't
apply to the chart as a whole, not each
facet
Note that in the full solution, the marker x values are independent of the main data.
I have tried using cowplot to draw it separately and overlay it, but that seems to:
affect the overall scale of the main plot, with the facet titles on the right being cropped
is not reliable in placing the markers at the exact location along the x scale
Any pointers welcome.
library(tidyverse)
mtcars2 <- rownames_to_column(mtcars, var = "car") %>%
mutate(make = stringr::word(car, 1)) %>%
filter(make >= "m" & make < "n")
markers <- data.frame(x = c(max(mtcars2$mpg), rep(runif(nrow(mtcars2), 1, max(mtcars2$mpg))), max(mtcars2$mpg))) %>%
mutate(name = paste0("marker # ", round(x)))
ggplot(mtcars2, aes()) +
# Main Plot
geom_tile(aes(x = mpg, y = car, fill = cyl), color = "white") +
# Add Markers
geom_point(data = markers, aes(x = x, y = "Merc450 SLC"), color = "red") +
# Marker Labels
geom_text(data = markers, aes(x = x, "Merc450 SLC",label = name), angle = 45, size = 2.5, hjust=0, nudge_x = -0.02, nudge_y = 0.15) +
facet_grid(make ~ ., scales = "free", space = "free") +
theme_minimal() +
theme(
# Facets
strip.background = element_rect(fill="Gray90", color = "white"),
panel.background = element_rect(fill="Gray95", color = "white"),
panel.spacing.y = unit(.7, "lines"),
plot.margin = margin(50, 20, 20, 20)
)
Perhaps draw two separate plots and assemble them together with patchwork:
library(patchwork)
p1 <- ggplot(markers, aes(x = x, y = 0)) +
geom_point(color = 'red') +
geom_text(aes(label = name),
angle = 45, size = 2.5, hjust=0, nudge_x = -0.02, nudge_y = 0.02) +
scale_y_continuous(limits = c(-0.01, 0.15), expand = c(0, 0)) +
theme_minimal() +
theme(axis.text = element_blank(),
axis.title = element_blank(),
panel.grid = element_blank())
p2 <- ggplot(mtcars2, aes(x = mpg, y = car, fill = cyl)) +
geom_tile(color = "white") +
facet_grid(make ~ ., scales = "free", space = "free") +
theme_minimal() +
theme(
strip.background = element_rect(fill="Gray90", color = "white"),
panel.background = element_rect(fill="Gray95", color = "white"),
panel.spacing.y = unit(.7, "lines")
)
p1/p2 + plot_layout(heights = c(1, 9))
It required some workaround with plot on different plot and using cowplot alignment function to align them on the same axis. Here is a solution
library(tidyverse)
library(cowplot)
# define a common x_axis to ensure that the plot are on same scales
# This may not needed as cowplot algin_plots also adjust the scale however
# I tended to do this extra step to ensure.
x_axis_common <- c(min(mtcars2$mpg, markers$x) * .8,
max(mtcars2$mpg, markers$x) * 1.1)
# Plot contain only marker
plot_marker <- ggplot() +
geom_point(data = markers, aes(x = x, y = 0), color = "red") +
# Marker Labels
geom_text(data = markers, aes(x = x, y = 0,label = name),
angle = 45, size = 2.5, hjust=0, nudge_x = 0, nudge_y = 0.001) +
# using coord_cartesian to set the zone of plot for some scales
coord_cartesian(xlim = x_axis_common,
ylim = c(-0.005, 0.03), expand = FALSE) +
# using theme_nothing from cow_plot which remove all element
# except the drawing
theme_nothing()
# main plot with facet
main_plot <- ggplot(mtcars2, aes()) +
# Main Plot
geom_tile(aes(x = mpg, y = car, fill = cyl), color = "white") +
coord_cartesian(xlim = x_axis_common, expand = FALSE) +
# Add Markers
facet_grid(make ~ ., scales = "free_y", space = "free") +
theme_minimal() +
theme(
# Facets
strip.background = element_rect(fill="Gray90", color = "white"),
panel.background = element_rect(fill="Gray95", color = "white"),
panel.spacing.y = unit(.7, "lines"),
plot.margin = margin(0, 20, 20, 20)
)
Then align the plot and plot them using cow_plot
# align the plots together
temp <- align_plots(plot_marker, main_plot, axis = "rl",
align = "hv")
# plot them with plot_grid also from cowplot - using rel_heights for some
# adjustment
plot_grid(temp[[1]], temp[[2]], ncol = 1, rel_heights = c(1, 8))
Created on 2021-05-03 by the reprex package (v2.0.0)
I am plotting a smooth to my data using geom_smooth and using geom_ribbon to plot shaded confidence intervals for this smooth. No matter what I try I cannot get a single legend that represents both the smooth and the ribbon correctly, i.e I am wanting a single legend that has the correct colours and labels for both the smooth and the ribbon. I have tried using + guides(fill = FALSE), guides(colour = FALSE), I also read that giving both colour and fill the same label inside labs() should produce a single unified legend.
Any help would be much appreciated.
Note that I have also tried to reset the legend labels and colours using scale_colour_manual()
The below code produces the below figure. Note that there are two curves here that are essentially overlapping. The relabelling and setting couours has worked for the geom_smooth legend but not the geom_ribbon legend and I still have two legends showing which is not what I want.
ggplot(pred.dat, aes(x = age.x, y = fit, colour = tagged)) +
geom_smooth(size = 1.2) +
geom_ribbon(aes(ymin = lci, ymax = uci, fill = tagged), alpha = 0.2, colour = NA) +
theme_classic() +
labs(x = "Age (days since hatch)", y = "Body mass (g)", colour = "", fill = "") +
scale_colour_manual(labels = c("Untagged", "Tagged"), values = c("#3399FF", "#FF0033")) +
theme(axis.title.x = element_text(face = "bold", size = 14),
axis.title.y = element_text(face = "bold", size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.text = element_text(size = 12))
The problem is that you provide new labels for the color-aesthetic but not for the fill-aesthetic. Consequently ggplot shows two legends because the labels are different.
You can either also provide the same labels for the fill-aesthetic (code option #1 below) or you can set the labels for the levels of your grouping variable ("tagged") before calling ggplot (code option #2).
library(ggplot2)
#make some data
x = seq(0,2*pi, by = 0.01)
pred.dat <- data.frame(x = c(x,x),
y = c(sin(x), cos(x)) + rnorm(length(x) * 2, 0, 1),
tag = rep(0:1, each = length(x)))
pred.dat$lci <- c(sin(x), cos(x)) - 0.4
pred.dat$uci <- c(sin(x), cos(x)) + 0.4
#option 1: set labels within ggplot call
pred.dat$tagged <- as.factor(pred.dat$tag)
ggplot(pred.dat, aes(x = x, y = y, color = tagged, fill = tagged)) +
geom_smooth(size = 1.2) +
geom_ribbon(aes(ymin = lci, ymax = uci), alpha = 0.2, color = NA) +
scale_color_manual(labels = c("untagged", "tagged"), values = c("#F8766D", "#00BFC4")) +
scale_fill_manual(labels = c("untagged", "tagged"), values = c("#F8766D", "#00BFC4")) +
theme_classic() + theme(legend.title = element_blank())
#option 2: set labels before ggplot call
pred.dat$tagged <- factor(pred.dat$tag, levels = 0:1, labels = c("untagged", "tagged"))
ggplot(pred.dat, aes(x = x, y = y, color = tagged, fill = tagged)) +
geom_smooth(size = 1.2) +
geom_ribbon(aes(ymin = lci, ymax = uci), alpha = 0.2, color = NA) +
theme_classic() + theme(legend.title = element_blank())
I am trying to make a boxplot with this basic code:
design=c("Red","Green","Blue")
actions=c("1","2","3","4","5","6","7","8")
proportion=(seq(1:240)+sample(1:500, 240, replace=T))/2000
df=data.frame(design, actions , proportion)
ggplot(df, aes(x=actions, y=proportion, fill=design)) +
geom_boxplot()+
xlab(TeX("group"))+
ylab("Y value")+
ggtitle("Y values for each group stratified by color")
Producing something like this:
I want to add horizontal lines for "true" Y values that are different for each group.
Does anyone have any tips for doing this? I don't know how to extract the width of each group of boxes, otherwise I could use geom_segment.
Here is a MWE with a non-grouped boxplot:
dBox <- data.frame(y = rnorm(10),group="1")
dBox=rbind(dBox,data.frame(y=rnorm(10),group="2"))
dLines <- data.frame(X =c(-0.36, 0.015),
Y = c(0.4, -0.2),
Xend = c(0.-0.015, 0.36),
Yend=c(0.4, -0.2),
group = c("True", "True"),
color = c("black", "red"))
ggplot(dBox, aes(x=0, y=y,fill=group)) +
geom_boxplot(outlier.shape = 1)+
geom_segment(data = dLines, aes(x = X, xend = Xend, y = Y, yend = Yend),color="red",size=1.5,linetype=1) +
theme(legend.background = element_rect(fill = "white", size = 0.1, linetype = "solid", colour = "black"))
This produces something like this:
However, it's difficult to make the geom_segments line up with the boxes exactly, and to then extend this to the grouped boxplot setting.
Thanks!
This can be done using a workaround with facets:
lines = data.frame(actions = 1:8, proportion=abs(rnorm(8)))
design=c("Red","Green","Blue")
actions=c("1","2","3","4","5","6","7","8")
proportion=(seq(1:240)+sample(1:500, 240, replace=T))/2000
df=data.frame(design, actions , proportion)
lines = data.frame(actions = 1:8, proportion=abs(rnorm(8)))
p = ggplot(df, aes(x=actions, y=proportion, fill=design)) +
geom_boxplot()+
xlab("group")+
ylab("Y value")+
ggtitle("Y values for each group stratified by color") +
facet_grid(~actions, scale='free_x') +
theme(
panel.spacing.x = unit(0, "lines"),
strip.background = element_blank(),
strip.text.x = element_blank())
p + geom_hline(aes(yintercept = proportion), lines)
You could probably fiddle around with removing the spaces between the facets to make it look more like what you intended.
Thanks to #eugene100hickey for pointing out how to remove spacing between facets.
theme(panel.spacing.x) can remove those pesky lines:
p + geom_hline(aes(yintercept = proportion), lines) +
theme(panel.spacing.x = unit(0, "lines"))
I have the following code:
df=data.frame(time=as.factor(rep(0.5:9.5,each=10)),
roi=rep(1:10,10),
area=runif(100, 5.0, 7.5))
df$time=factor(df$time, levels=rev(levels(df$time)))
ggplot(data=df, aes(x=factor(roi), y=time, fill = area)) +
theme_minimal() + coord_fixed(ratio=1) +
geom_tile(colour = NA, width = 1.5, height = 1) +
scale_fill_gradient(low="black",high="white")
Now, I want to remove the x-axis and add a new one to have the expected fig below. The x-axis will be divided into 4 parts for 4 segs with 39%,23%,23%,15% of axis length for Seg 1, Seg 2, Seg 3, Seg 4, respectively. Could anybody hava any idea to solve it. I apprecicate all response and am looking forward your answers.
Great thanks to Mark Heckmann for helpful answer to my problem. I would like to ask one more thing. I also want to modify the y-axis by "scale_y_discrete", the code ran well but the y-axis label did not meet my expectation. The code I ran is:
ggplot(data=df, aes(x=factor(roi), y=time, fill = area)) + theme_minimal() +coord_fixed(ratio=1) +geom_tile(colour = NA, width = 1.5, height = 1)+scale_fill_gradient(low="black",high="white") +scale_y_discrete(name="Time (min)",expand =c(0.01,0.1),breaks=c(1,2.5,5.0,7.5,10.0),labels=c(0,15,30,45,60))
Thank you very much!
You need to use annotation_custom to draw outside the plotting area.
#### your plot
library(ggplot2)
g <- ggplot(data=df, aes(x=factor(roi), y=time, fill = area)) +
theme_minimal() + coord_fixed(ratio=1) +
geom_tile(colour = NA, width = 1.5, height = 1) +
scale_fill_gradient(low="black",high="white")
Extra code:
library(grid)
# remove axis
g <- g + theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank()) +
scale_x_discrete(expand = c(0,0))
# calculate segment coordinates
segs <- c(.39, .23, .23, .15)
segs_center <- cumsum(segs) - segs/2
seg_ticks <- cumsum(segs)[1:3]
seg_labels <- paste("Seg", seq_along(segs))
# create graphicaal objects and gather as tree
grobs <- grobTree(linesGrob(c(0,1), c(.5,.5)),
segmentsGrob(x0=seg_ticks, x1=seg_ticks, y0=0, y1=1),
textGrob(x=segs_center, y=0,
label = seg_labels, hjust = .5, gp = gpar(cex =.7)))
# insert grobsTree in as annotation
g <- g + annotation_custom( grob = grobs,
ymin = -.2, ymax = .2,
xmin = .25, xmax = 10.75)
# override clipping for plotting outside of plotting area
gt <- ggplot_gtable(ggplot_build(g))
gt$layout$clip[gt$layout$name == "panel"] <- "off"
grid.newpage()
grid.draw(gt)
This is as good as I can get without going into custom annotation grobs.
library(ggplot2)
library(grid)
df=data.frame(time=as.factor(rep(0.5:9.5,each=10)),
roi=rep(1:10,10),area=runif(100, 5.0, 7.5))
df$time=factor(df$time, levels=rev(levels(df$time)))
p1 <- ggplot(data=df, aes(x=factor(roi), y=time, fill = area)) +
theme_minimal() +coord_fixed(ratio=1) +
geom_tile(colour = NA, width = 1.5, height = 1)+
scale_fill_gradient(low="black",high="white") +
scale_x_discrete(breaks = c(4,6,8,10),
labels = paste0("Seg",1:4)) +
theme(axis.title.x = element_blank(),
axis.ticks.x = element_line(size =1),
axis.text.x = element_text(hjust=c(2,1.5,1.5,1.5)),
plot.margin = unit(c(2,0,2,0), "lines"))
See here if you want to look into drawing the axis labels and tick marks customwise.