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I'm trying to simulate data for an experiment (learning purpose, self-taught) The purpose is to see how with the increase of distance (in cm) my variable decrease (I'm actually expecting that with the real data the decrease will be not linear). 5 replicate generated around my expected value, each indicated as e1, e2 etc.. and 4 distances indicated in cm

So this is the matrix: 

dis2 <- rnorm(5, mean = 0.25, sd = 0.01)
dis12 <- rnorm(5, mean = 0.22, sd = 0.01)
dis24 <- rnorm(5, mean = 0.19, sd = 0.01)
dis36 <- rnorm(5, mean = 0.16, sd = 0.01)

mat <- matrix(c(dis2, dis12, dis24, dis36), ncol=5, byrow = TRUE)
tmat <- t(mat)
dfmat <- as.data.frame(tmat)
colnames(dfmat) <- c("2cm", "12cm", "24cm", "36cm")
rownames(dfmat) <- c("e1", "e2", "e3", "e4", "e5")

Now I want to build a 3 column dataframe where each measure has the value but also if those values belong to e1, e2 etc.. and if the measure is relative to 2cm, 12 cm etc

The closest I could come is by melt()

list <- as.list(dfmat)
melted <- melt(list)

Here I can obtain the respective distance and value measure but not at which experiment (e1, e2 etc..) belong

How can I add this parameter? I've tried to add the (e1, e2 etc..) as a factor but still can not manage to melt the list correctly

Any help would be great

Stedy
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George Boccarella
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2 Answers2

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Using the tidyverse framework, we can move the rownames into a column then pivot appropriately.

library(dplyr)
library(tibble)
library(tidyr)

dfmat %>% 
  as.data.frame() %>%
  rownames_to_column("experiment") %>%
  gather('decrease', 'val', `2cm`:`36cm`)

   experiment decrease       val
1          e1      2cm 0.2602702
2          e2      2cm 0.2446041
3          e3      2cm 0.2652482
4          e4      2cm 0.2292223
5          e5      2cm 0.2431740
6          e1     12cm 0.2203435
7          e2     12cm 0.2324304
8          e3     12cm 0.2299671
9          e4     12cm 0.2113966
10         e5     12cm 0.2186454
11         e1     24cm 0.1847289
12         e2     24cm 0.1999656
13         e3     24cm 0.1766850
14         e4     24cm 0.1946892
15         e5     24cm 0.1902934
16         e1     36cm 0.1594713
17         e2     36cm 0.1574840
18         e3     36cm 0.1763698
19         e4     36cm 0.1651663
20         e5     36cm 0.1517848

That said, you may be able to skip the round-about way of making a test set with:

dat <- data.frame(
  experiment = rep(c("e1", "e2", "e3", "e4", "e5"), 4),
  decrease = rep(c("2cm", "12cm", "24cm", "36cm"), each = 5),
  val = c(dis2, dis12, dis24, dis36)
)

> dat
   experiment decrease       val
1          e1      2cm 0.2602702
2          e2      2cm 0.2446041
3          e3      2cm 0.2652482
4          e4      2cm 0.2292223
5          e5      2cm 0.2431740
6          e1     12cm 0.2203435
7          e2     12cm 0.2324304
8          e3     12cm 0.2299671
9          e4     12cm 0.2113966
10         e5     12cm 0.2186454
11         e1     24cm 0.1847289
12         e2     24cm 0.1999656
13         e3     24cm 0.1766850
14         e4     24cm 0.1946892
15         e5     24cm 0.1902934
16         e1     36cm 0.1594713
17         e2     36cm 0.1574840
18         e3     36cm 0.1763698
19         e4     36cm 0.1651663
20         e5     36cm 0.1517848
zack
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  • Do you also know why then I can't build a fitting line with geom_stath? `#First I've ordered the factor with increasing distance ndfmat$decreased <- factor(ndfmat$decrease, levels = c("2cm", "12cm", "24cm", "36cm")) ndfmat$decrease <- NULL` `library(ggplot2)` `ggplot(data=ndfmat, aes(x=ndfmat$decreased, y=ndfmat$val)) + geom_point() + geom_smooth()` – George Boccarella Sep 15 '18 at 08:13
0

Do you also know why then I can't build a fitting line with geom_stath? 

#First I've ordered the factor with increasing distance 
ndfmat$decreased <- factor(ndfmat$decrease, levels = c("2cm", "12cm", "24cm", "36cm"))
ndfmat$decrease <- NULL`


library(ggplot2) 
ggplot(data=ndfmat, aes(x=ndfmat$decreased, y=ndfmat$val)) +
geom_point() +
geom_smooth()
George Boccarella
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