如何更正我的代码以在 R 中使用 ggplot2 运行堆积条形图？

Question

My data includes 6 samples ( as rownames currently) and 24 columns each of which is named after different bacterial species, and the numbers are the relative abundances.

Here is the structure;

dput(sig_speciesstacked) 

structure(c("Control1", "Control2", "Control3", "Disease1", "Disease2", "Disease3", "0.32503", "0.55197", "1.23225", "0", "0", "0", "0.11568", "1.27372", "0.04306", "0", "0", "0", "0.78402", "0.99583", "0.03723", "0", "0", "0", "0.07664", "0.0932", "0.28018", "0", "0", "0", "0.29037", "0.74246", "0.3061", "0", "0", "0", "0.22328", "0.40351", "0.00416", "0", "0", "0", "0", "0", "0", "0.23779", "0.70807", "0.00891", "0.04852", "0.34497", "0.19266", "0", "0", "0", "0.26408", "0.05026", "0.0022", "0", "0", "0", "0.31206", "0.59428", "0.15606", "0", "0", "0", "0.13716", "0.55023", "0.4716", "0", "0", "0", "0.27194", "0.57013", "0.23164", "0", "0", "0", "6.84233", "2.18166", "0.6827", "0", "0", "0", "0", "0", "0", "0.94569", "0.0108", "0.06016", "0.32686", "0.04407", "1.02125", "0", "0", "0", "0", "0", "0", "0.51243", "0.10427", "1.48269", "0", "0", "0", "1.49594", "0.90364", "0.0081", "1.27002", "1.80154", "0.33065", "0", "0", "0", "2.40484", "0.36535", "3.79276", "0", "0", "0", "4.23202", "2.63742", "0.37963", "0", "0", "0", "0.38793", "0.81874", "0.04095", "0", "0", "0", "0", "0", "0", "1.04847", "0.08983", "0.02608", "0", "0", "0", "0.14408", "0.1637", "0.07754"), .Dim = c(6L, 24L), .Dimnames = list(c("1", "2", "3", "4", "5", "6"), c("Sample", "Alistipes_finegoldii", "Alistipes_indistinctus", "Alistipes_onderdonkii", "Alistipes_senegalensis", "Bacteroidales_bacterium_ph8", "Bifidobacterium_adolescentis", "Bifidobacterium_dentium", "Collinsella_aerofaciens", "Coprobacter_fastidiosus", "Coprococcus_comes", "Dorea_longicatena", "Eubacterium_hallii", "Eubacterium_rectale", "Fusobacterium_varium", "Lachnospiraceae_bacterium_3_1_46FAA", "Lactobacillus_mucosae", "Megasphaera_micronuciformis", "Odoribacter_splanchnicus", "Roseburia_hominis", "Ruminococcus_bromii", "Ruminococcus_callidus", "Streptococcus_parasanguinis", "Veillonella_atypica")))

I am trying to make a stacked bar chart showing the different abundances for the different samples ( 3 control and 3 diseases).

First I added a column name to the one containing my sample names, so there were then 25 columns in total. 1st one contains samples, 2:25 contain the abundances of the 24 different species.

 sig_speciesstacked <- cbind(Samples= rownames(sig_speciesstacked), sig_speciesstacked)

 print(colnames(sig_speciesstacked))

 rownames(sig_speciesstacked) <- c("1", "2", "3", "4", "5", "6").  

I already have installed and loaded reshape2. The code I run then is

 sig_speciesstackplot1 <- melt(sig_speciesstacked, id.vars = "Samples", variable.name = "species")

 pdf("Stackedbarplot.species.pdf", width = 6, height = 7)
 ggplot(sig_speciesstackplot1,aes(x=Samples, y=value, fill= species))+ geom_bar(stat = 
 "identity", position="fill")

The error I am met with is Error in FUN(X[[i]], ...) : object 'Samples' not found, then it will be abundance not found, then species not found.

Edit; I understand I have to rename aes(x=, y=) to the col names of sig_speciesstackplot1. However, this is not the correct format of the sig_speciesstackplot1 output following melt?

       Var1    Var2                 value
     1  1   Samples               Control1
     2  2   Samples               Control2
     3  3   Samples               Control3
     4  4   Samples               Disease1
     5  5   Samples               Disease2
     6  6   Samples               Disease3
     7  1   Alistipes_finegoldii    0.32503
     8  2   Alistipes_finegoldii    0.55197
     9  3   Alistipes_finegoldii    1.23225
     10 4   Alistipes_finegoldii    0

And so on, each of the 24 species is repeated 6 times with different abundance levels corresponding to the different samples.

Not sure why Var1 and Var2 were not renamed to "Samples" and "species" respectively from my line of code above, and why the output is like that.

And running the ggplot using aes(x = Var1 etc) gets a plot that is completely wrong.

Edit; For anybody having a similar issue, please do not use cbind. From an example on here, they made column 1 contain the sample names, hence why I used it. If you don't do this and just have the row names as the sample names, it will work fine. Thank you very much to those who helped below!

Answer 1

nice that you are posting here for the first time. I don't know if I understand your question correctly but here is my attempt in solving it.

Please note that my approach uses 'pipes' ( %>% ) and also the function pivot_longer from the package tidyverse instead of melt .

# load needed packge (includes ggplot2), install first if not installed yet
library("tidyverse")

# putting your data into an object
sig_speciesstacked <- structure(c(0.32503, 0.55197, 1.23225, 0, 0, 0, 0.11568, 1.27372, 0.04306, 0, 0, 0, 0.78402, 0.99583, 0.03723, 0, 0, 0, 0.07664, 0.0932, 0.28018, 0, 0, 0, 0.29037, 0.74246, 0.3061, 0, 0, 0, 0.22328, 0.40351, 0.00416, 0, 0, 0, 0, 0, 0, 0.23779, 0.70807, 0.00891, 0.04852, 0.34497, 0.19266, 0, 0, 0, 0.26408, 0.05026, 0.0022, 0, 0, 0, 0.31206, 0.59428, 0.15606, 0, 0, 0, 0.13716, 0.55023, 0.4716, 0, 0, 0, 0.27194, 0.57013, 0.23164, 0, 0, 0, 6.84233, 2.18166, 0.6827, 0, 0, 0, 0, 0, 0, 0.94569, 0.0108, 0.06016, 0.32686, 0.04407, 1.02125, 0, 0, 0, 0, 0, 0, 0.51243, 0.10427, 1.48269, 0, 0, 0, 1.49594, 0.90364, 0.0081, 1.27002, 1.80154, 0.33065, 0, 0, 0, 2.40484, 0.36535, 3.79276, 0, 0, 0, 4.23202, 2.63742, 0.37963, 0, 0, 0, 0.38793, 0.81874, 0.04095, 0, 0, 0, 0, 0, 0, 1.04847, 0.08983, 0.02608, 0, 0, 0, 0.14408, 0.1637, 0.07754), .Dim = c(6L, 23L), .Dimnames = list(c("Control1", "Control2", "Control3", "Disease1", "Disease2", "Disease3" ), c("Alistipes_finegoldii", "Alistipes_indistinctus", "Alistipes_onderdonkii", "Alistipes_senegalensis", "Bacteroidales_bacterium_ph8", "Bifidobacterium_adolescentis", "Bifidobacterium_dentium", "Collinsella_aerofaciens", "Coprobacter_fastidiosus", "Coprococcus_comes", "Dorea_longicatena", "Eubacterium_hallii", "Eubacterium_rectale", "Fusobacterium_varium", "Lachnospiraceae_bacterium_3_1_46FAA", "Lactobacillus_mucosae", "Megasphaera_micronuciformis", "Odoribacter_splanchnicus", "Roseburia_hominis", "Ruminococcus_bromii", "Ruminococcus_callidus", "Streptococcus_parasanguinis", "Veillonella_atypica")))

df_plot <- sig_speciesstacked %>% 
        # maling a data frame from your data
        data.frame() %>% 
        # use the matrix row names (your data) and put them into a column names 'type'
        rownames_to_column(var = "type") %>% 
        # pivot longer instead of melt
        pivot_longer(-type, names_to = "names", values_to = "value")

ggplot(data = df_plot,
       aes(x = names, y = value, group = type, fill = type)) + 
        geom_bar(stat = "identity", position="stack")

^{Created on 2019-11-25 by the reprex package (v0.3.0)}

---

Update

After clarification and looking at your code again, the solution seems simpler. You were on a good track, only that you didn't use the correct names from you 'melted' data for the plot, as @camille pointed out.

The aesthetics ( aes ) in ggplot need to refer to the column names in your data ( sig_speciesstackplot1 ). As you saw yourself, these are Var1 , Var2 , and value .

library("tidyverse")
library(reshape2)
#> 
#> Attaching package: 'reshape2'
#> The following object is masked from 'package:tidyr':
#> 
#>     smiths

# Your code
sig_speciesstacked <- structure(c(0.32503, 0.55197, 1.23225, 0, 0, 0, 0.11568, 1.27372, 0.04306, 0, 0, 0, 0.78402, 0.99583, 0.03723, 0, 0, 0, 0.07664, 0.0932, 0.28018, 0, 0, 0, 0.29037, 0.74246, 0.3061, 0, 0, 0, 0.22328, 0.40351, 0.00416, 0, 0, 0, 0, 0, 0, 0.23779, 0.70807, 0.00891, 0.04852, 0.34497, 0.19266, 0, 0, 0, 0.26408, 0.05026, 0.0022, 0, 0, 0, 0.31206, 0.59428, 0.15606, 0, 0, 0, 0.13716, 0.55023, 0.4716, 0, 0, 0, 0.27194, 0.57013, 0.23164, 0, 0, 0, 6.84233, 2.18166, 0.6827, 0, 0, 0, 0, 0, 0, 0.94569, 0.0108, 0.06016, 0.32686, 0.04407, 1.02125, 0, 0, 0, 0, 0, 0, 0.51243, 0.10427, 1.48269, 0, 0, 0, 1.49594, 0.90364, 0.0081, 1.27002, 1.80154, 0.33065, 0, 0, 0, 2.40484, 0.36535, 3.79276, 0, 0, 0, 4.23202, 2.63742, 0.37963, 0, 0, 0, 0.38793, 0.81874, 0.04095, 0, 0, 0, 0, 0, 0, 1.04847, 0.08983, 0.02608, 0, 0, 0, 0.14408, 0.1637, 0.07754), .Dim = c(6L, 23L), .Dimnames = list(c("Control1", "Control2", "Control3", "Disease1", "Disease2", "Disease3" ), c("Alistipes_finegoldii", "Alistipes_indistinctus", "Alistipes_onderdonkii", "Alistipes_senegalensis", "Bacteroidales_bacterium_ph8", "Bifidobacterium_adolescentis", "Bifidobacterium_dentium", "Collinsella_aerofaciens", "Coprobacter_fastidiosus", "Coprococcus_comes", "Dorea_longicatena", "Eubacterium_hallii", "Eubacterium_rectale", "Fusobacterium_varium", "Lachnospiraceae_bacterium_3_1_46FAA", "Lactobacillus_mucosae", "Megasphaera_micronuciformis", "Odoribacter_splanchnicus", "Roseburia_hominis", "Ruminococcus_bromii", "Ruminococcus_callidus", "Streptococcus_parasanguinis", "Veillonella_atypica")))

sig_speciesstackplot1 <- melt(sig_speciesstacked, id.vars = "Samples", variable.name = "species")

# Correct plot
ggplot(sig_speciesstackplot1,
       aes(x=Var1, y=value, fill= Var2))+ 
        geom_bar(stat = "identity", position="stack") +
        theme(legend.position="bottom")

^{Created on 2019-11-25 by the reprex package (v0.3.0)}

---

Update 2

If you want them 'stacked' as a percentage, you can use position = "fill" like so:

ggplot(sig_speciesstackplot1,
       aes(x=Var1, y=value, fill= Var2))+ 
        geom_bar(stat = "identity", position="fill") +
        theme(legend.position="bottom")

^{Created on 2019-11-25 by the reprex package (v0.3.0)}

---

Update 3

After re-examining the OPs code and the comments below I want to share the following.

The OP used reshape2::melt() on a matrix with rownames . This issue is discussed here: Why reshape2's Melt cannot capture rownames in the transformation?

Below, I compare the behaviour of reshape2::melt() for a matrix and a data.frame . The latter one shows the intended behaviour.

# OPs code
sig_speciesstacked <- structure(c(0.32503, 0.55197, 1.23225, 0, 0, 0, 0.11568, 1.27372, 0.04306, 0, 0, 0, 0.78402, 0.99583, 0.03723, 0, 0, 0, 0.07664, 0.0932, 0.28018, 0, 0, 0, 0.29037, 0.74246, 0.3061, 0, 0, 0, 0.22328, 0.40351, 0.00416, 0, 0, 0, 0, 0, 0, 0.23779, 0.70807, 0.00891, 0.04852, 0.34497, 0.19266, 0, 0, 0, 0.26408, 0.05026, 0.0022, 0, 0, 0, 0.31206, 0.59428, 0.15606, 0, 0, 0, 0.13716, 0.55023, 0.4716, 0, 0, 0, 0.27194, 0.57013, 0.23164, 0, 0, 0, 6.84233, 2.18166, 0.6827, 0, 0, 0, 0, 0, 0, 0.94569, 0.0108, 0.06016, 0.32686, 0.04407, 1.02125, 0, 0, 0, 0, 0, 0, 0.51243, 0.10427, 1.48269, 0, 0, 0, 1.49594, 0.90364, 0.0081, 1.27002, 1.80154, 0.33065, 0, 0, 0, 2.40484, 0.36535, 3.79276, 0, 0, 0, 4.23202, 2.63742, 0.37963, 0, 0, 0, 0.38793, 0.81874, 0.04095, 0, 0, 0, 0, 0, 0, 1.04847, 0.08983, 0.02608, 0, 0, 0, 0.14408, 0.1637, 0.07754), .Dim = c(6L, 23L), .Dimnames = list(c("Control1", "Control2", "Control3", "Disease1", "Disease2", "Disease3" ), c("Alistipes_finegoldii", "Alistipes_indistinctus", "Alistipes_onderdonkii", "Alistipes_senegalensis", "Bacteroidales_bacterium_ph8", "Bifidobacterium_adolescentis", "Bifidobacterium_dentium", "Collinsella_aerofaciens", "Coprobacter_fastidiosus", "Coprococcus_comes", "Dorea_longicatena", "Eubacterium_hallii", "Eubacterium_rectale", "Fusobacterium_varium", "Lachnospiraceae_bacterium_3_1_46FAA", "Lactobacillus_mucosae", "Megasphaera_micronuciformis", "Odoribacter_splanchnicus", "Roseburia_hominis", "Ruminococcus_bromii", "Ruminococcus_callidus", "Streptococcus_parasanguinis", "Veillonella_atypica")))
sig_speciesstacked <- cbind(Samples= rownames(sig_speciesstacked), sig_speciesstacked)
rownames(sig_speciesstacked) <- c("1", "2", "3", "4", "5", "6")

# Using reshapse2::melt on a matrix
sig_speciesstackplot1 <- reshape2::melt(sig_speciesstacked,
                              id.vars = "Samples", variable.name = "species")
head(sig_speciesstackplot1)
#>   Var1    Var2    value
#> 1    1 Samples Control1
#> 2    2 Samples Control2
#> 3    3 Samples Control3
#> 4    4 Samples Disease1
#> 5    5 Samples Disease2
#> 6    6 Samples Disease3

# Using reshapse2::melt on a data.frame with stringsAsFactors = F
sig_speciesstackplot1 <- reshape2::melt(as.data.frame(sig_speciesstacked,
                                                      stringsAsFactors = F),
                              id.vars = "Samples", variable.name = "species")
head(sig_speciesstackplot1)
#>    Samples              species   value
#> 1 Control1 Alistipes_finegoldii 0.32503
#> 2 Control2 Alistipes_finegoldii 0.55197
#> 3 Control3 Alistipes_finegoldii 1.23225
#> 4 Disease1 Alistipes_finegoldii       0
#> 5 Disease2 Alistipes_finegoldii       0
#> 6 Disease3 Alistipes_finegoldii       0

^{Created on 2019-11-26 by the reprex package (v0.3.0)}