ChromoMap Error in 1:nrow(temp.df) : argument of length 0

Question

[kousi31]

I am trying to plot the distribution of genes on chromosome using chromoMap.
I prepared a chromosome_file. txt as per manual

NC_037545.1     1       202105980   
NC_037546.1     1       188952477
NC_037547.1     1       175630833

and Annotation_file.txt as

LOC112581744    NC_037545.1     6566415 6567888   
LOC112582356   NC_037545.1     8234378 8238149   
LOC112582960    NC_037545.1    12240957        12245030   
LOC112582972    NC_037545.1     12499447     12505618

I am getting as Error in 1:nrow(temp.df) : argument of length 0

I tried searching Google for answers an found an answer as

it's the classic gotcha of, with a matrix with one dimension of length 1, without drop=FALSE, R converts a matrix to a vector

I think it is bcoz of the chromosome start position being one in all columns. I don't know where to specify drop=FALSE

I am new to R. Kindly help.

[Ram]

Do you have a variable named temp.df? If not, you need to find out where this error happens (which function call) and check its input parameters - if one or more of them is a data.frame, ensure all subsetting operations are done in this manner

df[row_filter_if_any, col_filter_if_any, drop = FALSE]

Let's say you need the first row and/or first column, it could be

df[1, , drop = FALSE] #only rows 1
df[, 1, drop = FALSE] # only col 1

If you're not sure how many rows or columns would be returned, use the general format specified above.

[kousi31]

The software takes the file directly from the working directory. If I use data.frame to import the data, it is not recognizing the object.

> setwd("~/lr/chromomap/")
> library(chromoMap)
> chromoMap("chromosome_file.txt","de_lncrna.annotation")
********************************** __ __ ************
** __**|__ * __* __ * __ __ * __ *|  |  |* __ * __ **
**|__**|  |*|  *|__|*|  |  |*|__|*|  |  |*|_ |*|__|**
***********************************************|   **
*************** by Lakshay Anand ********************
OUTPUT: 
Number of Chromosome sets: 1 
Number of Chromosomes in set  1 : 25 
Processing data.. 
Number of annotations in data set  1 : 121 
Error in 1:nrow(temp.df) : argument of length 0

I tried to use data.frame

> chromosome.f <- data.frame("chromosome_file.txt", row.names = NULL, stringsAsFactors = T)
> annotation.f <- data.frame("de_lncrna.annotaion", row.names = NULL,stringsAsFactors = T)
> chromoMap("chromosome.f","annotation.f")
********************************** __ __ ************
** __**|__ * __* __ * __ __ * __ *|  |  |* __ * __ **
**|__**|  |*|  *|__|*|  |  |*|__|*|  |  |*|_ |*|__|**
***********************************************|   **
*************** by Lakshay Anand ********************
OUTPUT: 
Number of Chromosome sets: 1 
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'chromosome.f': No such file or directory

According to the manual once input file is created, directly import the text file

Once you have your input files ready, begin creating chromosomes plots like a pro. The simplest annotation plot can be created using the following command:

>library(chromoMap)
> chromoMap("chromosome_file.txt","annotation_file.txt")
  

[Ram]

The software looks really badly written, I wonder if CRAN does any QC before accepting packages. Is this the best package you can find for your purposes?

In any case, I think you'd be better off emailing the author at the email mentioned in the manual (although there are two emails specified in the manual and one of them looks like a typo, but to be safe, add both of them as recipients.)