Masi Masi - 26 days ago 7
R Question

How to R present two colsums with ggplot stat_summary?

I think R designed tool for the taks is

ggplot2 stat_summary
so I rejected
barplot
because of the linked thread in the body.

The problem here is the declaration of R table structure with column headers
ECG 1
and
ECG 2
for the sums
M.1.sum
and
M.2.sum
, respectively, I think.
I try to do it with
means.long <- melt(M.1.sum, M.2.sum)
.
Each item,
M.1.sum
and
M.2.sum
, has corresponding row-wise ids in
ids
which should also included in the data structure itself, I think.
My proposal for its table column and row declarations is with
aes(x=ids, y=value)
where
value
is about the sums in
ggplot
declaration.
Code

library('ggplot2')
library('reshape2')

M <- structure(c(-0.21, -0.205, -0.225, -0.49, -0.485, -0.49,
-0.295, -0.295, -0.295, -0.56, -0.575, -0.56, -0.69, -0.67,
-0.67, -0.08, -0.095, -0.095), .Dim = c(3L, 6L))
M2 <- structure(c(-0.121, -0.1205, -0.1225, -0.149, -0.485, -0.49,
-0.295, -0.295, -0.295, -0.56, -0.1575, -0.56, -0.69, -0.67,
-0.117, -0.08, -0.1095, -0.1095), .Dim = c(3L, 6L))

ids <- seq(1,6)
M.1.sum <- colSums(M)
M.2.sum <- colSums(M2)

# http://stackoverflow.com/q/22305023/54964
means.long <- melt(M.1.sum, M.2.sum)
ggplot(means.long, aes(x=ids, y=value ))+ # ,fill=factor(ids))) +
stat_summary(fun.y=mean, geom="bar",position=position_dodge(1)) +
scale_fill_discrete(name="ECG",
breaks=c(1, 2),
labels=c("1", "2"))+
stat_summary(fun.ymin=min,fun.ymax=max,geom="errorbar",
color="grey80",position=position_dodge(1), width=.2) +
xlab("ID")+ylab("Sum potential")

#depreciated because stat_summary designed for the case
#barplot(M.1.sum, ids)
#barplot(M.2.sum, ids)


Output does not look right

enter image description here

Expected output: 6x two columns side by side with legend of two items

Not sure how to use this one
fill=factor(ids)))
because I did not label any columns in the table.
How can you better make the table?

Testing errorbars for the answer



Pseudocode

y.sd = sd(each col M) # TODO which data structure suitable for ggplot here?
# http://www.ats.ucla.edu/stat/r/pages/ggplot2_errorbar.htm
ggplot(means, aes(x = col, y = mean, fill = source)) +
geom_bar(stat = 'identity', position = 'dodge') +
geom_errorbar(data = means,
mapping = aes(x = col, y = means,
ymin = means - y.sd,
ymax = means + y.sd),
size=1,
color="red", width=.4)


Testing non-incremental x-axis for the answer



I put
ids
(
= c(1, 777, 2, 4, 5, 6)
) to x-axis which can be range from 777 to 1.
Output wrong now

enter image description here

R: 3.3.1

OS: Debian 8.5

Answer

With ggplot, it is essential to have a single data frame with everything in it (at least for a single plotting layer, e.g., all the bars in a plot). You create a data frame of the column sums, and then try to use external vectors for the id and the grouping, which makes things difficult.

This is how I would do it:

means = rbind(
    data.frame(mean = colSums(M), source = "M", col = 1:ncol(M)),
    data.frame(mean = colSums(M2), source = "M2", col = 1:ncol(M2))
)

means$col = factor(means$col)
## one nice data frame with everything needed for the plot    
means
#       mean source col
# 1  -0.6400      M   1
# 2  -1.4650      M   2
# 3  -0.8850      M   3
# 4  -1.6950      M   4
# 5  -2.0300      M   5
# 6  -0.2700      M   6
# 7  -0.3640     M2   1
# 8  -1.1240     M2   2
# 9  -0.8850     M2   3
# 10 -1.2775     M2   4
# 11 -1.4770     M2   5
# 12 -0.2990     M2   6

ggplot(means, aes(x = col, y = mean, fill = source)) +
    geom_bar(stat = 'identity', position = 'dodge')

enter image description here

You seem to want error bars too. I have no idea what would define those error bars - if you look at geom_errorbar it expects aesthetics ymin and ymax. If you calculate whatever values you want and add them as column to the data frame above, adding the error bar to the plot should be easy.