Masi Masi - 16 days ago 7
R Question

2x4 Lattice Barchart minimally in R?

Two data files of two different measurement sessions:

ECG
and
B ECG
.
Each data file contains male and female.
I want to do 2 column x 4 row Lattice Barchart minimally in R where the following is a draft of the interface.
I can do 2x2 barchart, see code below.
There must be some more minimal way than manually just adding more and more lines to the end of the code, which is difficult to control.

ECG B.ECG
female female
Sinus
Arr/AHB
Digoxin arr
Furosemide arr
ECG B.ECG
male male
Sinus
Arr/AHB
Digoxin arr
Furosemide arr


Data ecg.csv

female Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.0,0.0,0.0,0.0,0.0,12.0,0.0
Arr/AHB,1.0,0.0,0.0,0.1,0.0,0.0,20.9,0.0
Digoxin arr,1.0,0.0,0.0,0.2,0.0,0.0,10.8,0.0
Furosemide arr,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
,,,,,,,,
male Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.0,0.0,0.0,0.0,0.0,4.0,0.0
Arr/AHB,1.0,0.0,0.0,0.0,0.0,0.0,24.0,0.0
Digoxin arr,1.0,0.0,0.0,0.0,0.0,0.0,11.0,0.0
Furosemide arr,1.0,0.0,0.0,0.0,0.0,0.0,3.0,0.0


Data b.ecg.csv

female Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.2,0.2,0.0,0.0,0.0,11.7,0.0
Arr/AHB,1.2,0.0,1.8,3.8,0.0,0.0,15.1,0.1
Digoxin arr,0.5,0.2,0.0,1.0,0.0,0.0,4.3,0.0
Furosemide arr,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
,,,,,,,,
male Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.0,0.0,0.0,0.0,0.0,4.0,0.0
Arr/AHB,1.0,3.2,0.0,4.3,0.0,0.0,16.5,0.0
Digoxin arr,1.0,0.0,0.7,0.8,0.0,0.0,9.5,0.0
Furosemide arr,1.0,0.0,0.0,0.0,0.0,0.0,3.0,0.0


Code which can do 2x2 barchart but difficult to expand to 2 col x 4 row barchart about 1) read data, and 2) apply Lattice barchart

library("gridExtra")
library("lattice")
library("reshape2")

data.n <- read.csv("ecg.csv", sep=",", header = TRUE)[1:2,1:7]
rownames(data.n) <- read.csv("ecg.csv", sep=",", header = TRUE)[1:2,1]
data.n.female <- read.csv("ecg.csv", sep=",", header = TRUE)[1:2,1:7]
rownames(data.n.female) <- read.csv("ecg.csv", sep=",", header = TRUE)[1:2,1]
data.n.male <- read.csv("ecg.csv", sep=",", header = TRUE)[1:2,1:7]
rownames(data.n.male) <- read.csv("ecg.csv", sep=",", header = TRUE)[1:2,1]

data.b <- read.csv("b.ecg.csv", sep=",", header = TRUE)[1:2,1:7]
rownames(data.b) <- read.csv("b.ecg.csv", sep=",", header = TRUE)[1:2,1]
data.b.female <- read.csv("b.ecg.csv", sep=",", header = TRUE)[1:2,1:7]
rownames(data.b.female) <- read.csv("b.ecg.csv", sep=",", header = TRUE)[1:2,1]
data.b.male <- read.csv("b.ecg.csv", sep=",", header = TRUE)[1:2,1:7]
rownames(data.b.male) <- read.csv("b.ecg.csv", sep=",", header = TRUE)[1:2,1]

# http://stackoverflow.com/a/40693458/54964
#1
data.n[] <- lapply(data.n, function(x) as.numeric(as.character(x)))
data.n$type <- "ecg"
data.n$ID <- rownames(data.n)

data.b[] <- lapply(data.b, function(x) as.numeric(as.character(x)))
data.b$type <- "b ecg"
data.b$ID <- rownames(data.b)

dat <- rbind(data.n[names(data.b)], data.b)
# Arrange data for plotting
dat.m <- melt(dat)

barchart(variable ~ value|ID, groups=type, data=dat.m,
auto.key=list(space='right'),
origin=0
)

#2
data.n.female[] <- lapply(data.n.female, function(x) as.numeric(as.character(x)))
data.n.female$gender <- "female"
data.n.female$ID <- rownames(data.n.female)

data.n.male[] <- lapply(data.n.male, function(x) as.numeric(as.character(x)))
data.n.male$gender <- "male"
data.n.male$ID <- rownames(data.n.male)

data.b.female[] <- lapply(data.b.female, function(x) as.numeric(as.character(x)))
data.b.female$gender <- "female"
data.b.female$ID <- rownames(data.b.female)

data.b.male[] <- lapply(data.b.male, function(x) as.numeric(as.character(x)))
data.b.male$gender <- "male"
data.b.male$ID <- rownames(data.b.male)

dat.2 <- rbind(data.n.female[names(data.n.male)],
data.b.female[names(data.b.male)],
data.n.male,
data.b.male)
dat.2$type <- rep(c("ECG", "B ECG"), each=2)
dat.2.m <- melt(dat.2, id=c("ID", "gender", "type"))
barchart(variable ~ value|ID+type, groups=gender, data=dat.2.m, auto.key=list(space='right'),
origin=0)


Fig. 1 Output of 2x2 Lattice barchart code

enter image description here

Troubleshooting the answer here for my system



Output with the code 1 in the answer


Using male.Nij, gender, group as id variables Error in
layout_base(data, rows, drop = drop) : At least one layer must contain
all variables used for facetting Calls: <Anonymous> ...
facet_train_layout.grid -> layout_grid -> layout_base Execution halted



Output 2 with the code

Error in +geom_bar(stat = "identity", position = position_dodge()) :
invalid argument to unary operator
Execution halted

# Code
datm$male.Nij <- factor(datm$male.Nij, levels=lvs)
ggplot(datm, aes(variable, value, fill=gender))
+ geom_bar(stat="identity", position = position_dodge())
+ facet_grid(male.Nij ~ group)
# + facet_grid(factor(male.Nij, levels=lvs) ~ group)
+ coord_flip()


System info

> library(ggplot2)
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] ggplot2_2.1.0

loaded via a namespace (and not attached):
[1] colorspace_1.3-0 scales_0.4.1 plyr_1.8.4 gtable_0.2.0
[5] Rcpp_0.12.7 grid_3.3.2 munsell_0.4.3


We noticed there is some differences in the handling
+
by
ggplot2
versions.
Final line to get the code work in the described system

ggplot(datm, aes(variable, value, fill=gender)) + geom_bar(stat="identity", position = position_dodge()) + facet_grid(male.Nij ~ group)


R: 3.3.2 backports

OS: Debian 8.5

Answer

I think the best approach is to combine the data, and reshape for plotting

# Your data
# ECG
fem <- read.csv( text=
"female Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.0,0.0,0.0,0.0,0.0,12.0,0.0
Arr/AHB,1.0,0.0,0.0,0.1,0.0,0.0,20.9,0.0
Digoxin arr,1.0,0.0,0.0,0.2,0.0,0.0,10.8,0.0
Furosemide arr,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0")

male <- read.csv( text=
"male Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.0,0.0,0.0,0.0,0.0,4.0,0.0
Arr/AHB,1.0,0.0,0.0,0.0,0.0,0.0,24.0,0.0
Digoxin arr,1.0,0.0,0.0,0.0,0.0,0.0,11.0,0.0
Furosemide arr,1.0,0.0,0.0,0.0,0.0,0.0,3.0,0.0")

# Add gender grouping variable
fem$gender <- "female"
male$gender <- "male"
fem$group <- male$group <- "ECG"

# ECG  b
fem2 <- read.csv( text=
"female Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.2,0.2,0.0,0.0,0.0,11.7,0.0
Arr/AHB,1.2,0.0,1.8,3.8,0.0,0.0,15.1,0.1
Digoxin arr,0.5,0.2,0.0,1.0,0.0,0.0,4.3,0.0
Furosemide arr,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0")

male2 <- read.csv( text=
"male Nij,N11,N22,N33,N44,N21,N31,N32,N123
Sinus,1.0,0.0,0.0,0.0,0.0,0.0,4.0,0.0
Arr/AHB,1.0,3.2,0.0,4.3,0.0,0.0,16.5,0.0
Digoxin arr,1.0,0.0,0.7,0.8,0.0,0.0,9.5,0.0
Furosemide arr,1.0,0.0,0.0,0.0,0.0,0.0,3.0,0.0")

fem2$gender <- "female"
male2$gender <- "male"
fem2$group <- male2$group <- "ECG b"

Combine data and reshape

# you will need to check they are in the right order
dat <- rbind(setNames(fem, names(male)), male, 
             setNames(fem2, names(male)), male2)

# reshape data for plotting
library(reshape2)
datm <- melt(dat)

Lattice plot

library(lattice)

lvs = unique(dat$male.Nij) # for ordering facets    
barchart(variable ~ value|group + factor(male.Nij, levels=lvs), groups=gender, 
              data=datm, auto.key=list(space='right'), origin=0)

ggplot2 plot

library(ggplot2) # v2.1.0.9001

ggplot(datm, aes(variable, value, fill=gender)) + 
  geom_bar(stat="identity", position = position_dodge()) +
  facet_grid(factor(male.Nij, levels=lvs) ~ group) +
      coord_flip()

For earlier ggplot2 (v2.1.0) versions you may need to set the factor levels outside of facet_grid

datm$male.Nij <- factor(datm$male.Nij, levels=lvs)

 ggplot(datm, aes(variable, value, fill=gender)) + 
        geom_bar(stat="identity", position = position_dodge()) + 
        facet_grid(male.Nij ~ group) + 
        coord_flip()

enter image description here

and the full code for easy copy-pasting here.

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