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I am trying to make a heatmap of a sites vs. species abundances matrix. With thanks to Maurits Evers for some of this code, I am still not able to run it without the error message:
Setting row names on a tibble is deprecated.Error in
row.names<-.data.frame(*tmp*, value = list(Site = c("AwarukuLower", : invalid 'row.names' length
It was suggested tidyverse & tibbles may be the issue. I uninstalled packages tibble & tidyverse and installed the devtools readr package instead. I am still getting the same error message and can't figure out how to fix this. Data attached.
library(readr)
devtools::install_github("tidyverse/readr") #to install readr without tidyverse
bank_mean_wide_sp <- read.csv("/Users/Chloe/Desktop/Environmental Data Analysis/EDA.working.directory/bank_mean_wide.csv")
log_mean_wide_sp <- read_csv("/Users/Chloe/Desktop/Environmental Data Analysis/EDA.working.directory/log_mean_wide.csv")
as.matrix(bank_mean_wide_sp)
as.matrix(log_mean_wide_sp)
Store Site information as rownames
logdf <- log_mean_wide_sp;
base::row.names(logdf) <- log_mean_wide_sp[, 1];
Remove non-numeric column
logdf <- logdf[, -1];
Use as.matrix to convert data.frame to matrix
logmap <- heatmap(
as.matrix(logdf),
col = cm.colors(256),
scale = "column",
margins = c(5, 10),
xlab = "species", ylab = "Site",
main = "heatmap(<Auckland Council MCI data 1999, habitat:bank>, ..., scale = \"column\")")
Returns the error message as mentioned above:
Setting row names on a tibble is deprecated.Error in
row.names<-.data.frame(*tmp*, value = list(Site = c("AwarukuLower", : invalid 'row.names' length
Alternatively, I tried to run the code without first 3 lines, and used as.numeric and as.matrix to convert data.frame to numeric matrix. This also did not work.
as.matrix(logdf)
logmap <- heatmap(as.numeric(logdf),
col = cm.colors(256),
scale = "column",
margins = c(5, 10),
xlab = "species", ylab = "Site",
main = "heatmap(<Auckland Council MCI data 1999, habitat:bank>, ..., scale = \"column\")")
Returns this second error:
Error in heatmap(as.numeric(logdf), col = cm.colors(256), scale = "column", : (list) object cannot be coerced to type 'double'
832
Method 1 : using rownames() A data frame's rows can be accessed using rownames() method in the R programming language. We can specify the new row names using a vector of numerical or strings and assign it back to the rownames() method.
While a tibble can have row names (e.g., when converting from a regular data frame), they are removed when subsetting with the [ operator. A warning will be raised when attempting to assign non- NULL row names to a tibble.
Tibbles vs data frames There are two main differences in the usage of a data frame vs a tibble: printing, and subsetting. Tibbles have a refined print method that shows only the first 10 rows, and all the columns that fit on screen. This makes it much easier to work with large data.
Tibbles are data. frames that are lazy and surly: they do less (i.e. they don't change variable names or types, and don't do partial matching) and complain more (e.g. when a variable does not exist). This forces you to confront problems earlier, typically leading to cleaner, more expressive code.
Your error messages has 2 parts
- Setting row names on a tibble is deprecated.
This means setting row names on tibble is deprecated. It still works as of now but will be removed in future. See this https://github.com/tidyverse/tibble/issues/123.
- Error in
row.names<-.data.frame(*tmp*, value = list(Site = c("AwarukuLower", : invalid 'row.names' length
This is error saying that the length of row.names that you are setting is not equal to total no of rows you have in your data frame.
The error is in reading your csv file, your csv file has first column as row name but you are reading it as normal column. Read it correctly by using
log_mean_wide_sp<-read.csv("log_mean_wide.csv",row.names = 1)
Then do the below steps as you are doing
logdf<-log_mean_wide_sp
logmap <- heatmap(
as.matrix(logdf),
col = cm.colors(256),
scale = "column",
margins = c(5, 10),
xlab = "species", ylab = "Site",
main = "heatmap(<Auckland Council MCI data 1999, habitat:bank>, ..., scale = \"column\")")
It will give below image as output
80
I would recommend creating a matrix version of the numeric part of your data frame:
log_mean_mat <- as.matrix(log_mean_wide_sp[,-1])
You shouldn't have issues setting the row-names for this:
row.names(log_mean_mat) <- log_mean_wide_sp[,1]
I personally strongly prefer the heatmap.2 function for heatmaps (in the gplots package) over the base function, but here's what should work using the base code:
heatmap(log_mean_mat,
col = cm.colors(256),
scale = "column",
margins = c(5, 10),
xlab = "species", ylab = "Site",
main = "heatmap(<Auckland Council MCI data 1999, habitat:bank>, ..., scale = \"column\")")
Site Acarina Acroperla Amphipoda Austroclima Austrolestes Ceratopogonidae
AwarukuLower 0 0 1 0 0 0
AwarukuMid 1 20 6 0 0 0
NukumeaLower 0 44 1 0 0 1
NukumeaUpper 1 139 9 2 1 0
VaughanLower 1 110 112 1 0 0
VaughanMid 2 44 12 2 1 0
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