Generating a plot with rafalib open.
Have a dataset with a column labeled "Tissue". The entire table is in object "b". "hc" contains a hclust of the distribution of the numeric values of "b".
When I run:
myplclust(hc, xlab="distance",main="Hierarchical Clustering Dendrogram",labels=b$Tissue,lab.col=as.fumeric(b$Tissue),cex=0.5)
RStudio responds with:
Error in as.fumeric(b$Tissue) : 'x' must be a character
What's going on here? I've reset R multiple times. I have rafalib installed and active.
SOLVED:
The names I was entering under this function were being recognized as data rather than values for some reason. By converting my list to a vector with as.vector inside of the as.fumeric function, the problem was solved.
The correct code now looks like;
myplclust(hc, xlab="distance",main="Hierarchical Clustering Dendrogram",labels=b$Tissue,lab.col=as.fumeric(as.vector(b$Tissue)),cex=0.5)
Related
I got the error message:
Error: object 'x' not found
Or a more complex version like
Error in mean(x) :
error in evaluating the argument 'x' in selecting a method for function 'mean': Error: object 'x' not found
What does this mean?
The error means that R could not find the variable mentioned in the error message.
The easiest way to reproduce the error is to type the name of a variable that doesn't exist. (If you've defined x already, use a different variable name.)
x
## Error: object 'x' not found
The more complex version of the error has the same cause: calling a function when x does not exist.
mean(x)
## Error in mean(x) :
## error in evaluating the argument 'x' in selecting a method for function 'mean': Error: object 'x' not found
Once the variable has been defined, the error will not occur.
x <- 1:5
x
## [1] 1 2 3 4 5
mean(x)
## [1] 3
You can check to see if a variable exists using ls or exists.
ls() # lists all the variables that have been defined
exists("x") # returns TRUE or FALSE, depending upon whether x has been defined.
Errors like this can occur when you are using non-standard evaluation. For example, when using subset, the error will occur if a column name is not present in the data frame to subset.
d <- data.frame(a = rnorm(5))
subset(d, b > 0)
## Error in eval(expr, envir, enclos) : object 'b' not found
The error can also occur if you use custom evaluation.
get("var", "package:stats") #returns the var function
get("var", "package:utils")
## Error in get("var", "package:utils") : object 'var' not found
In the second case, the var function cannot be found when R looks in the utils package's environment because utils is further down the search list than stats.
In more advanced use cases, you may wish to read:
The Scope section of the CRAN manual Intro to R and demo(scoping)
The Non-standard evaluation chapter of Advanced R
While executing multiple lines of code in R, you need to first select all the lines of code and then click on "Run".
This error usually comes up when we don't select our statements and click on "Run".
Let's discuss why an "object not found" error can be thrown in R in addition to explaining what it means. What it means (to many) is obvious: the variable in question, at least according to the R interpreter, has not yet been defined, but if you see your object in your code there can be multiple reasons for why this is happening:
check syntax of your declarations. If you mis-typed even one letter or used upper case instead of lower case in a later calling statement, then it won't match your original declaration and this error will occur.
Are you getting this error in a notebook or markdown document? You may simply need to re-run an earlier cell that has your declarations before running the current cell where you are calling the variable.
Are you trying to knit your R document and the variable works find when you run the cells but not when you knit the cells? If so - then you want to examine the snippet I am providing below for a possible side effect that triggers this error:
{r sourceDataProb1, echo=F, eval=F}
# some code here
The above snippet is from the beginning of an R markdown cell. If eval and echo are both set to False this can trigger an error when you try to knit the document. To clarify. I had a use case where I had left these flags as False because I thought i did not want my code echoed or its results to show in the markdown HTML I was generating. But since the variable was then used in later cells, this caused an error during knitting. Simple trial and error with T/F TRUE/FALSE flags can establish if this is the source of your error when it occurs in knitting an R markdown document from RStudio.
Lastly: did you remove the variable or clear it from memory after declaring it?
rm() removes the variable
hitting the broom icon in the evironment window of RStudio clearls everything in the current working environment
ls() can help you see what is active right now to look for a missing declaration.
exists("x") - as mentioned by another poster, can help you test a specific value in an environment with a very lengthy list of active variables
I had a similar problem with R-studio. When I tried to do my plots, this message was showing up.
Eventually I realised that the reason behind this was that my "window" for the plots was too small, and I had to make it bigger to "fit" all the plots inside!
Hope to help
I'm going to add this on here even though it's not a new question as it comes quite highly in the search results for the error:
As mentioned above, re checking syntax, if you're using dplyr, make sure you have all the %>% pipes at the end of the lines above the error, otherwise the contents of anything like a select statement won't pass down into the next part of the code block.
I'm new at R and I'm currently trying to get some statistical data from a file. It is a large set of data in txt tab-delimited file. While importing the file I had no problem and all of the data is shown correctly as a table in rstudio. However, when I'm trying to make any sort of calculations using colsums,
> colSums("Wages and salaries")
Error in colSums("Wages and salaries") : 'x' must be an array of at
least two dimensions
I do receive an error
x' must be an array of at least two dimensions.
"Wages and Salaries" is the name of the column I'm trying to get the sum of.
Using V1 or any other column name that was created by r gives me another error
> colSums(V2)
Error in is.data.frame(x) : object 'V2' not found
The way I'm importing the file is
rm(list=ls())
filename <- read.delim("~/filename.txt", header=FALSE)`
> is.data.frame(filename)
[1] TRUE
This gives me a matrix type data table with rows and columns the same way excel would show me the data.
The reason I'm trying to get a sum of all of the numbers in column is to later get sum of several different columns.
I'm very new at R and I could not find an answer to my question as most of the examples are using just a very small set of data that was created in the r.
In R you can access a column in 2 ways:
filename["Wages and salaries"]
or
filename$`Wages and salaries`
So, please try :
colSums(filename["Wages and salaries"])
I have a column of a few thousand prison facility names that have been scraped from the internet, some of which contain a "/" character. I'm running a ggplot loop that plots COVID infections in each facility, but the ggsave() function breaks whenever it hits a facility with the / because it thinks I am changing the file directory.
Is there a way to change the "/" character in my column to a "-"? I tried using gsub() but to no avail:
(1)
fix$Name <- gsub("\/"","-",gsub$Name)
I get the following error (2)
Error in gsub$Name : object of type 'closure' is not subsettable
I initially tried to just run (3)
fix$Name <- gsub("/","-",gsub$Name)
But I am fairly sure that I need an escape character, hence code line (1).
fix$Name is a character string.
If anyone has an insight that would be greatly appreciated! Thanks!
I have tried multiple variations of the rename function in dplyr.
I have a data frame called from a database called alldata, and a column within the data frame named WindDirection:N. I am trying to rename it as Wind Direction. I understand creating variable names containing spaces is not a good practice, but I want it to be named as such to improve readability for a selectInput list in shiny, and even if I settle for renaming it WindDirection I am getting all of the same error messages.
I have tried:
rename(alldata, Wind Direction = WindDirection:N)
which gives the error message:
Error: unexpected symbol in "rename(alldata, Wind Direction"
rename(alldata, `Wind Direction` = `WindDirection:N`)
which does not give an error message, but also does not rename the variable
rename(alldata, "Wind Direction" = "WindDirection:N")
which gives the error message:
Error: Arguments to rename must be unquoted variable names. Arguments Wind Direction are not.
I then tried the same 3 combinations of the reverse order (because I know that is how plyr works even though I do not call it to be used using the library command earlier in my code) putting the old variable first and the new variable 2nd with similar error messages.
I then tried to specify the package as I have 1 example below and tried all 6 combinations again.
dplyr::rename(alldata, `Wind Direction` = `WindDirection:N`)
to similar error messages as the first time.
I have used the following thread as an attempt to do this myself.
Replacement for "rename" in dplyr
as agenis pointed out, my mistake was not redefining the dataframe after renaming the variable.
So where I had
dplyr::rename(alldata,Wind Direction=WindDirection:N)
I should have
alldata <- dplyr::rename(alldata,Wind Direction=WindDirection:N)
Yesterday I posted this question on Stats Exchange and based on the response I got, I decided to do some analysis using R's src() function. It's part of the "sensitivity" package.
I installed the package with no trouble, and then tried the following command:
sens <- src(seminars, REV, rank=TRUE, nboot=100)
sens is a new variable to store the results of the test
seminars is a data frame that I imported from a CSV file using the read.csv() command
REV is the name of a variable/column in seminars and my desired response variable
When I ran the command, I got the following error:
Error in data.frame(Y = y, X) : object 'REV' not found
Any thoughts?
From the documentation of src
y: a vector containing the responses corresponding to the design
of experiments (model output variables).
The input needs to be a vector (apparently) and you're attempting to pass in a name (and not even quoting the name at that). Since REV isn't defined (I'm guessing due to the error message) in the global environment it doesn't know what to do.
From reading the documentation it sounds like what you want to do is pass sensitivity[,-which(colnames(sensitivity) == "REV")] (just the design matrix - you don't want to include the responses) in as x and sensitivity[,"REV"] in as y.
This error is linked to the fact that the data.frame X=seminars include factors with 0 value, which produce an error while constructing the regression coefficient. You can first remove them as they don't contribute to the variance of the output.