Ordering x-axis in ggplot2 boxplot using computed statistic - r

I have some data that I want to display as a box plot using ggplot2. It's basically counts, stratified by two other variables. Here's an example of the data (in reality there's a lot more, but the structure is the same):
TAG Count Condition
A 5 1
A 6 1
A 6 1
A 6 2
A 7 2
A 7 2
B 1 1
B 2 1
B 2 1
B 12 2
B 8 2
B 10 2
C 10 1
C 12 1
C 13 1
C 7 2
C 6 2
C 10 2
For each Tag, there are a fixed number of observations in condition 1, and condition 2 (here it's 3, but in the real data it's much more). I want a box plot like the following ('s' is a dataframe arranged as above):
ggplot(s, aes(x=TAG, y=Count, fill=factor(Condition))) + geom_boxplot()
This is fine, but I want to be able to order the x-axis by the p-value from a Wilcoxon test for each Tag. For example, with the above data, the values would be (for the tags A,B, and C respectively):
> wilcox.test(c(5,6,6),c(6,7,7))$p.value
[1] 0.1572992
> wilcox.test(c(1,2,2),c(12,8,10))$p.value
[1] 0.0765225
> wilcox.test(c(10,12,13),c(7,6,10))$p.value
[1] 0.1211833
Which would induce the ordering A,C,B on the x-axis (largest to smallest). But I don't know how to go about adding this information into my data (specifically, attaching a p-value at just the tag level, rather than adding a whole extra column), or how to use it to change the x-axis order. Any help greatly appreciated.

Here is a way do it. The first step is to calculate the p-values for each TAG. We do this by using ddply which splits the data by TAG, and calculates the p-value using the formula interface to wilcox.test. The plot statement reorders the TAG based on its p-value.
library(ggplot2); library(plyr)
dfr2 <- ddply(dfr, .(TAG), transform,
pval = wilcox.test(Count ~ Condition)$p.value)
qplot(reorder(TAG, pval), Count, fill = factor(Condition), geom = 'boxplot',
data = dfr2)

Related

Plotting mean values of groups in a dataframe in R

I have conducted a study with triplicates (SampleID) for each sample (Sample) on different time points.
Now, I want to plot the means of the triplicates for the characteristic "Aerobic".
I want to plot for example the development of amount of aerobic bacteria over time. Therefore, I need to calculate the means (and the standard deviation) of the triplicates and then plot these means in the graph. Here, I could imagine to use a geom_line or geom_point diagram.
SampleID Sample Aerobic Anaerobic Day
[Factor] [Factor] [num] [num] [num]
1 V1.1.K1 V1.1.K 0.610063430 0.05146154 1
2 V1.1.K2 V1.1.K 0.740887757 0.02115290 1
3 V1.1.K3 V1.1.K 0.683726217 0.04270182 1
4 V1.1.N1 V1.1.N 0.432019752 0.35722350 1
5 V1.1.N2 V1.1.N 0.515792694 0.41357935 1
6 V1.14.K16 V1.14.K 0.038141335 0.84496088 14
7 V1.14.K17 V1.14.K 0.042078682 0.76523093 14
8 V1.14.K18 V1.14.K 0.009594763 0.90767637 14
9 V1.14.N0 V1.14.N 0.513100502 0.10618731 14
10 V1.14.W16 V1.14.W 0.483710571 0.32765968 14
How should i do this?
I tried it with the following code
plot <- mydata %>%
group_by(Sample) %>%
mutate(Mean=mean(Aerobic)) %>%
ggplot(aes(x=Day, y=Aerobic)) +
geom_point()
If I google the questions I get only information about how to calculate the mean alone, but not to set up a new table with the means for the different variables.
Is there something like
calc_mean_by_group ??
You would help me a lot :)
Simple base-R solution for calculating the means:
tapply(X = foo$Aerobic, INDEX = foo$Sample, FUN = mean)
("foo" being the name of your data.frame)

Scatterplot with R from text file with log scale

I have data saved in a text file with couple thousands line. Each line only has one value. Like this
52312
2
3
4
5
7
9
4
5
3
The first value is always roughly 10.000 times bigger than all the other values.
I can read in the data with data<-read.table("data.txt")
When I just use plot(data) all the data have the same y-value, resulting in a line, where the x values just represent the values given from the data.
What I want, however, is that the x-value represents the linenumber and y-value the actual data. So for the above example my values would be (1,52312), (2,2), (3,3), (4,4), (5,5), (6,7), (7,9), (8,4), (9,5), (10,3).
Also, since the first value is way higher than all the other values, I'd like to use a log scale for the y-axis.
Sorry, very new to R.
set.seed(1000)
df = data.frame(a=c(9999999,sample(2:78,77,replace = F)))
plot(x=1:nrow(df), y=log(df$a))
i) set.seed(1000) helps you reproduce the same random numbers from sample() each time you run this code. It makes code reproducible.
ii) type ?sample in R console for documentation.
iii) since you wanted the x-axis to be linenumber - I create it using ":" operator. 1:3 = 1,2,3. Similarily I created a "id" index using 1:nrow(df) which will create based on the dimension of your data.
iv) for log ,just use it simple :). read more about ?plot and its parameters
Try this:
df
x y
1 1 52312
2 2 2
3 3 3
4 4 4
5 5 5
6 6 7
7 7 9
8 8 4
9 9 5
10 10 3
library(ggplot2)
ggplot(df, aes(x, y)) + geom_point(size=2) + scale_y_log10()

Creating stacked barplots in R using different variables

I am a novice R user, hence the question. I refer to the solution on creating stacked barplots from R programming: creating a stacked bar graph, with variable colors for each stacked bar.
My issue is slightly different. I have 4 column data. The last column is the summed total of the first 3 column. I want to plot bar charts with the following information 1) the summed total value (ie 4th column), 2) each bar is split by the relative contributions of each of the three column.
I was hoping someone could help.
Regards,
Bernard
If I understood it rightly, this may do the trick
the following code works well for the example df dataframe
df <- a b c sum
1 9 8 18
3 6 2 11
1 5 4 10
23 4 5 32
5 12 3 20
2 24 1 27
1 2 4 7
As you don't want to plot a counter of variables, but the actual value in your dataframe, you need to use the goem_bar(stat="identity") method on ggplot2. Some data manipulation is necessary too. And you don't need a sum column, ggplot does the sum for you.
df <- df[,-ncol(df)] #drop the last column (assumed to be the sum one)
df$event <- seq.int(nrow(df)) #create a column to indicate which values happaned on the same column for each variable
df <- melt(df, id='event') #reshape dataframe to make it readable to gpglot
px = ggplot(df, aes(x = event, y = value, fill = variable)) + geom_bar(stat = "identity")
print (px)
this code generates the plot bellow

Histograms in R with a "more" categorie, similar to MS Excel

Consider the following frequency data:
> table(income)
income
3 5 6 7 8 5000
2 7 2 2 2 1
When I type >hist(income) I get the following histogram
So as you can see, the fact that most income values are concentrated around 5 and there is one value quite distant from the others makes the histogram not look very good. MS Excel can consider the 5000 value as of another category, so the data would like this instead:
> table(income)
income
3 5 6 7 8 more
2 7 2 2 2 1
So plotting this as a histogram would look much better, so you can see the frequency within a shorter range:
Is there anyway to do this either with the hist() function or others functions from lattice or ggplot2? I do however, don't want to overwrite the values that exceed a certain threshold, so as I do lose any information.
Thanks a lot!
Data generation:
income <- c(rep(3,2), rep(5,7), rep(6,2), rep(7,2), rep(8,2), 5000)
Function for preparing data for plotting:
nice.data <- function(x, threshold=10){
x[x>threshold] <- "More"
x
}
Plotting:
library(ggplot2)
ggplot() + geom_histogram(aes(x=nice.data(income))) + xlab("Income")
Result:

R rank points in plot

I have a question about plots. For example we have variable a and b, we plot this in R and you get the point. Now, I want to make a range of best/highest point. Is there a way to generate a ranking in the point? I thought maybe something with mean?
Thanks!
a<- c(1,3,7,5,3,8,4,5,3,6,9,4,2,6,3)
b<- c(5,3,7,2,7,2,5,2,7,3,6,2,1,1,9)
plot(a,b)
Based on your comment to get the positions of the points with the 5 highest b values, use order:
order(b,decreasing=T)[1:5]
[1] 15 3 5 9 11
And you can use this to get the relevant a and b values:
a[order(b,decreasing=T)[1:5]]
[1] 3 7 3 3 9
b[order(b,decreasing=T)[1:5]]
[1] 9 7 7 7 6
You can use this also to highlight them in the plot:
high <- order(b,decreasing=T)[1:5]
col <- rep("black",length(b))
col[high] <- "red"
plot(a,b,col=col)
Note that there is some overplotting here (2 values at (3,7))

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