I wonder if there is the possibility to change the fill main colour according to a categorical variable
Here is a reproducible example
df = data.frame(x = c(rnorm(10, mean = 0),
rnorm(10, mean = 3)),
y = c(rnorm(10, mean = 0),
rnorm(10, mean = 3)),
grp = c(rep('a', times = 10),
rep('b', times = 10)),
val = rep(1:10, times = 2))
ggplot(data = df,
aes(x = x,
y = y)) +
geom_point(pch = 21,
aes(color = grp,
fill = val,
size = val))
Of course it is easy to change the circle colour/shape, according to the variable grp, but I'd like to have the a group in shades of red and the b group in shades of blue.
I also thought about using facets, but don't know if the fill gradient can be changed for the two panels.
Anyone knows if that can be done, without gridExtra?
Thanks!
I think there are two ways to do this. The first is using the alpha aesthetic for your val column. This is a quick and easy way to accomplish your goal but may not be exactly what you want:
ggplot(data = df,
aes(x = x,
y = y)) +
geom_point(pch = 21,
aes(alpha=val,
fill = grp,
size = val)) + theme_minimal()
The second way would be to do something similar to this post: Vary the color gradient on a scatter plot created with ggplot2. I edited the code slightly so its not a range from white to your color of interest but from a lighter color to a darker color. This requires a little bit of work and using the scale_fill_identity function which basically takes a variable that has the colors you want and maps them directly to each point (so it doesn't do any scaling).
This code is:
#Rescale val to [0,1]
df$scaled_val <- rescale(df$val)
low_cols <- c("firebrick1","deepskyblue")
high_cols <- c("darkred","deepskyblue4")
df$col <- ddply(df, .(grp), function(x)
data.frame(col=apply(colorRamp(c(low_cols[as.numeric(x$grp)[1]], high_cols[as.numeric(x$grp)[1]]))(x$scaled_val),
1,function(x)rgb(x[1],x[2],x[3], max=255)))
)$col
df
ggplot(data = df,
aes(x = x,
y = y)) +
geom_point(pch = 21,
aes(
fill = col,
size = val)) + theme_minimal() +scale_fill_identity()
Thanks to this other post I found a way to visualize the fill bar in the legend, even though that wasn't what I meant to do.
Here's the ouptup
And the code
df = data.frame(x = c(rnorm(10, mean = 0),
rnorm(10, mean = 3)),
y = c(rnorm(10, mean = 0),
rnorm(10, mean = 3)),
grp = factor(c(rep('a', times = 10),
rep('b', times = 10)),
levels = c('a', 'b')),
val = rep(1:10, times = 2)) %>%
group_by(grp) %>%
mutate(scaledVal = rescale(val)) %>%
ungroup %>%
mutate(scaledValOffSet = scaledVal + 100*(as.integer(grp) - 1))
scalerange <- range(df$scaledVal)
gradientends <- scalerange + rep(c(0,100,200), each=2)
ggplot(data = df,
aes(x = x,
y = y)) +
geom_point(pch = 21,
aes(fill = scaledValOffSet,
size = val)) +
scale_fill_gradientn(colours = c('white',
'darkred',
'white',
'deepskyblue4'),
values = rescale(gradientends))
Basically one should rescale fill values (e.g. between 0 and 1) and separate them using another order of magnitude, provided by the categorical variable grp.
This is not what I wanted though: the snippet can be improved, of course, to make the whole thing less manual, but still lacks the simple usual discrete fill legend.
Related
I couldn't find out how to do this anywhere so I thought I would post the solution now that I've figured it out.
I created a simple chart with labels based on a data set in long format (see below for dat). There are two lines and the labels overlap. I would like to move the labels for the upper chart up and for the lower chart down.
library(dplyr)
library(ggplot2)
library(tidyr)
# sample data
dat <- data.frame(
x = seq(1, 10, length.out = 10),
y1 = seq(1, 5, length.out = 10),
y2 = seq(1, 6, length.out = 10))
# convert to long format
dat <- dat %>%
gather(var, value, -x)
# plot it
ggplot(data = dat, aes(x = x, y = value, color = var)) +
geom_line() +
geom_label(aes(label = value))
To move the labels in opposite directions, one can create a step function in nudge_y to multiply the upper line's labels by +1 times a nudge factor and the multiply the lower line's labels by -1 times the nudge factor:
# move labels in opposite directions
ggplot(data = dat, aes(x = x, y = value, color = var)) +
geom_line() +
geom_label(aes(label = value),
nudge_y = ifelse(dat$var == "y2", 1, -1) * 1)
This produces the following chart with adjusted labels.
I'm trying to plot 2 sets of data points and a single line in R using ggplot.
The issue I'm having is with the legend.
As can be seen in the attached image, the legend applies the lines to all 3 data sets even though only one of them is plotted with a line.
I have melted the data into one long frame, but this still requires me to filter the data sets for each individual call to geom_line() and geom_path().
I want to graph the melted data, plotting a line based on one data set, and points on the remaining two, with a complete legend.
Here is the sample script I wrote to produce the plot:
xseq <- 1:100
x <- rnorm(n = 100, mean = 0.5, sd = 2)
x2 <- rnorm(n = 100, mean = 1, sd = 0.5)
x.lm <- lm(formula = x ~ xseq)
x.fit <- predict(x.lm, newdata = data.frame(xseq = 1:100), type = "response", se.fit = TRUE)
my_data <- data.frame(x = xseq, ypoints = x, ylines = x.fit$fit, ypoints2 = x2)
## Now try and plot it
melted_data <- melt(data = my_data, id.vars = "x")
p <- ggplot(data = melted_data, aes(x = x, y = value, color = variable, shape = variable, linetype = variable)) +
geom_point(data = filter(melted_data, variable == "ypoints")) +
geom_point(data = filter(melted_data, variable == "ypoints2")) +
geom_path(data = filter(melted_data, variable == "ylines"))
pushViewport(viewport(layout = grid.layout(1, 1))) # One on top of the other
print(p, vp = viewport(layout.pos.row = 1, layout.pos.col = 1))
You can set them manually like this:
We set linetype = "solid" for the first item and "blank" for others (no line).
Similarly for first item we set no shape (NA) and for others we will set whatever shape we need (I just put 7 and 8 there for an example). See e.g. http://www.r-bloggers.com/how-to-remember-point-shape-codes-in-r/ to help you to choose correct shapes for your needs.
If you are happy with dots then you can use my_shapes = c(NA,16,16) and scale_shape_manual(...) is not needed.
my_shapes = c(NA,7,8)
ggplot(data = melted_data, aes(x = x, y = value, color=variable, shape=variable )) +
geom_path(data = filter(melted_data, variable == "ylines") ) +
geom_point(data = filter(melted_data, variable %in% c("ypoints", "ypoints2"))) +
scale_colour_manual(values = c("red", "green", "blue"),
guide = guide_legend(override.aes = list(
linetype = c("solid", "blank","blank"),
shape = my_shapes))) +
scale_shape_manual(values = my_shapes)
But I am very curious if there is some more automated way. Hopefully someone can post better answer.
This post relied quite heavily on this answer: ggplot2: Different legend symbols for points and lines
I have the following code:
library("ggplot2")
set.seed(12351234)
names <- factor(rep(paste("C", 1:10, sep = "_"), each = 10))
time <- rep(1:10, 10)
outcome <- rnorm(mean = 1e7, sd = 1e7, n = length(time))
outcome <-ifelse(outcome < 0, 0, outcome)
data.toy <- data.frame(names, time, outcome)
ggplot(data = data.toy, aes(y = outcome, x = time)) + geom_bar(stat = "identity", aes(fill = names)) + scale_x_continuous(breaks = unique(data.toy$time))
and it produces the following image: http://picpaste.com/data_toy-OR0jVHj5.png
I am wondering if there is a way to remove the horizontal "gray" space between the bars on the x-axis (the space that the arrows are pointing at). I suspect I am using this geom incorrectly as time is not categorical and there is a more appropriate geom for this.
this is my first stack overflow post and I am a relatively new R user, so please go gently!
I have a data frame with three columns, a participant identifier, a condition (factor with 2 levels either Placebo or Experimental), and an outcome score.
set.seed(1)
dat <- data.frame(Condition = c(rep("Placebo",10),rep("Experimental",10)),
Outcome = rnorm(20,15,2),
ID = factor(rep(1:10,2)))
I would like to construct a bar plot with two bars with the mean outcome score for each condition and the standard deviation as an error bar. I would like to then overlay lines connecting points for each participant's score in each condition. So the plot displays the individual response as well as the group mean.If it is also possible I would like to include an axis break.
I don't seem to be able to find any advice in other threads, apologies if I am repeating a question.
Many Thanks.
p.s. I realise that presenting data in this way will not be to everyones tastes. It is for a specific requirement!
This ought to work:
library(ggplot2)
library(dplyr)
dat.summ <- dat %>% group_by(Condition) %>%
summarize(mean.outcome = mean(Outcome),
sd.outcome = sd(Outcome))
ggplot(dat.summ, aes(x = Condition, y = mean.outcome)) +
geom_bar(stat = "identity") +
geom_errorbar(aes(ymin = mean.outcome - sd.outcome,
ymax = mean.outcome + sd.outcome),
color = "dodgerblue", width = 0.3) +
geom_point(data = dat, aes(x = Condition, y = Outcome),
color = "firebrick", size = 1.2) +
geom_line(data = dat, aes(x = Condition, y = Outcome, group = ID),
color = "firebrick", size = 1.2, alpha = 0.5) +
scale_y_continuous(limits = c(0, max(dat$Outcome)))
Some people are better with ggplot's stat functions and arguments than I am and might do it differently. I prefer to just transform my data first.
set.seed(1)
dat <- data.frame(Condition = c(rep("Placebo",10),rep("Experimental",10)),
Outcome = rnorm(20,15,2),
ID = factor(rep(1:10,2)))
dat.w <- reshape(dat, direction = 'wide', idvar = 'ID', timevar = 'Condition')
means <- colMeans(dat.w[, 2:3])
sds <- apply(dat.w[, 2:3], 2, sd)
ci.l <- means - sds
ci.u <- means + sds
ci.width <- .25
bp <- barplot(means, ylim = c(0,20))
segments(bp, ci.l, bp, ci.u)
segments(bp - ci.width, ci.u, bp + ci.width, ci.u)
segments(bp - ci.width, ci.l, bp + ci.width, ci.l)
segments(x0 = bp[1], x1 = bp[2], y0 = dat.w[, 2], y1 = dat.w[, 3], col = 1:10)
points(c(rep(bp[1], 10), rep(bp[2], 10)), dat$Outcome, col = 1:10, pch = 19)
Here is a method using the transfomations inside ggplot2
ggplot(dat) +
stat_summary(aes(x=Condition, y=Outcome, group=Condition), fun.y="mean", geom="bar") +
stat_summary(aes(x=Condition, y=Outcome, group=Condition), fun.data="mean_se", geom="errorbar", col="green", width=.8, size=2) +
geom_line(aes(x=Condition, y=Outcome, group=ID), col="red")
I am making boxplots with ggplot with data that is classified by 2 factor variables. I'd like to have the box sizes reflect sample size via varwidth = TRUE but when I do this the boxes overlap.
1) Some sample data with a 3 x 2 structure
data <- data.frame(group1= sample(c("A","B","C"),100, replace = TRUE),group2= sample(c("D","E"),100, replace = TRUE) ,response = rnorm(100, mean = 0, sd = 1))
2) Default boxplots: ggplot without variable width
ggplot(data = data, aes(y = response, x = group1, color = group2)) + geom_boxplot()
I like how the first level of grouping is shown.
Now I try to add variable widths...
3) ...and What I get when varwidth = TRUE
ggplot(data = data, aes(y = response, x = group1, color = group2)) + geom_boxplot(varwidth = T)
This overlap seems to occur whether I use color = group2 or group = group2 in both the main call to ggplot and in the geom_boxplot statement. Fussing with position_dodge doesn't seem to help either.
4) A solution I don't like visually is to make unique factors by combining my group1 and group2
data$grp.comb <- paste(data$group1, data$group2)
ggplot(data = data, aes(y = response, x = grp.comb, color = group2)) + geom_boxplot()
I prefer having things grouped to reflect the cross classification
5) The way forward:
I'd like to either a)figure out how to either make varwidth = TRUE not cause the boxes to overlap or b)manually adjusted the space between the combined groups so that boxes within the 1st level of grouping are closer together.
I think your problem can be solved best by using facet_wrap.
library(ggplot2)
data <- data.frame(group1= sample(c("A","B","C"),100, replace = TRUE), group2=
sample(c("D","E"),100, replace = TRUE) ,response = rnorm(100, mean = 0, sd = 1))
ggplot(data = data, aes(y = response, x = group2, color = group2)) +
geom_boxplot(varwidth = TRUE) +
facet_wrap(~group1)
Which gives:
A recent update to ggplot2 makes it so that the code provided by #N Brouwer in (3) works as expected:
# library(devtools)
# install_github("tidyverse/ggplot2")
packageVersion("ggplot2") # works with v2.2.1.9000
library(ggplot2)
set.seed(1234)
data <- data.frame(group1= sample(c("A","B","C"), 100, replace = TRUE),
group2= sample(c("D","E"), 100, replace = TRUE),
response = rnorm(100, mean = 0, sd = 1))
ggplot(data = data, aes(y = response, x = group1, color = group2)) +
geom_boxplot(varwidth = T)
(I'm a new user and can't post images inline)
fig 1
This question has been answered here ggplot increase distance between boxplots
The answer involves using the position = position_dodge() argument of geom_boxplot().
For your example:
data <- data.frame(group1= sample(c("A","B","C"),100, replace = TRUE), group2=
sample(c("D","E"),100, replace = TRUE) ,response = rnorm(100, mean = 0, sd = 1))
ggplot(data = data, aes(y = response, x = group1, color = group2)) +
geom_boxplot(position = position_dodge(1))