Hi Stack Overflow community,
I have a dataset:
conc branch length stage factor
1 1000 3 573.5 e14 NRG4
2 1000 7 425.5 e14 NRG4
3608 1000 44 5032.0 P10 NRG4
3609 1000 0 0.0 P10 NRG4
FYI
> str(dframe1)
'data.frame': 3940 obs. of 5 variables:
$ conc : Factor w/ 6 levels "0","1","10","100",..: 6 6 6 6 6 6 6 6 6 6 ...
$ branch: int 3 7 5 0 1 0 0 4 1 1 ...
$ length: num 574 426 204 0 481 ...
$ stage : Factor w/ 8 levels "e14","e16","e18",..: 1 1 1 1 1 1 1 1 1 1 ...
$ factor: Factor w/ 2 levels "","NRG4": 2 2 2 2 2 2 2 2 2 2 ...
I would like to create facetted line graphs, plotting the mean +/- standard error of the mean
I have tried experimenting and building a ggplot from others (here and on the web).
I have successfully used scripts that will make bargraphs this way:
errbar.ggplot.facets <- ggplot(dframe1, aes(x = conc, y = length))
### function to calculate the standard error of the mean
se <- function(x) sd(x)/sqrt(length(x))
### function to be applied to each panel/facet
my.fun <- function(x) {
data.frame(ymin = mean(x) - se(x),
ymax = mean(x) + se(x),
y = mean(x))}
g.err.f <- errbar.ggplot.facets +
stat_summary(fun.y = mean, geom = "bar",
fill = clrs.hcl(48)) +
stat_summary(fun.data = my.fun, geom = "linerange") +
facet_wrap(~ stage) +
theme_bw()
print(g.err.f)
In fact, I have created facetted line graphs with this script:
`ggplot(data=dframe1, aes(x=conc, y = length, group = stage)) +
geom_line() + facet_wrap(~stage)`
image: postimg.org/image/ebpdc0sb7
However, I used a transformed dataset of only means, SEM in another column, but I don't know how to add them.
Given the complexity (for me) of the bargraphs + error line scripts above, I have not yet been able to integrate/synthesize these into something I need.
In this case, the colour is not important to have.
P.S. I apologise for the long thread (and perhaps the overkill on some details). This is my first online R question, so not sure of correct etiquette. Thank you all in advance for being so helpful!
Darian
In case your dataframe has a column for the mean and the se you could do something like this:
library("dplyr")
library("ggplot2")
# Create a dummydataframe with columns mean and se
df <- mtcars %>%
group_by(gear, cyl) %>%
summarise(mean_mpg = mean(mpg), se_mpg = se(mpg))
ggplot(df, aes(x = gear, y = mean_mpg)) +
geom_bar(stat = "identity") +
geom_errorbar(aes(ymin = mean_mpg - se_mpg, ymax = mean_mpg + se_mpg)) +
facet_wrap(~cyl)