plot error x y length difference

Question

[yusuf]

I have used this command

plot(log.norm.counts.a[,1:2], cex=.1)

but it gives following error

Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ

I can't make changes in the file.

anyone know how to solve, like skip ids which are missing.

[Ram]

You can make changes in the object you create by reading the file. Please search Stack Overflow to understand how to manipulate data frames.

[Corentin]

Can you show us a subset of your dataframe ?

The error message say that you do not have the same length between log.norm.counts.a[,1] and log.norm.counts.a[,2]. Have you tried to check the content of these two columns ?

Answer 1

[kashiff007]

Try this code. It should solve your problem

data <- read.csv("~/Desktop/my_data.csv", header=TRUE)
dim(data)
rnames <- data[,1]                            # assign labels in column 1 to "rnames"
mat_data <- data.matrix(data[,2:ncol(data)])  # transform column 2-5 into a matrix
rownames(mat_data) <- rnames        
mat_data         # this is only matrix now with dimension n rows and 12 column
x1 <- mat_data[,1:6]  # assigning first 6 cols to x1
y1 <- mat_data[,7:12]  # assigning seventh to 12 cols to x1

install.packages("matrixStats")
library(matrixStats)
x2 <- rowSds(x1)     # standard deviation from x1
y2 <- rowSds(y1)    #  standard deviation from y1


plot(x2,y2) # for plot

[yusuf]

it worked

thanks :)

[Ram]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.

Answer 2

[yusuf]

Hi thankyou for your reply

I want to plot SD of two groups of files, with different length

I have slightly solved this by

Y2 <- as.data.table((log.norm.counts.a[,1:6]), keep.rownames = "geneid")
X2 <- as.data.table((log.norm.counts.b[,1:6]), keep.rownames = "geneid")
m3 <- merge(X2,Y2,by=c("geneid"))
head(m3)

dim(m3)
[1] 1500    13


X1 <- m3[,2:7]
head(X1[,1:6])
Y1 <- m3[,8:13]
head(Y1)

but when i try

a<- as.data.table(rowSds(X1))
b<- as.data.table(rowSds(Y1))
plot(a,b)

or

plot(rowSds(m3[,2:7]),rowSds(m3[,8:13]))

it gives error

Error in rowVars(x, rows = rows, cols = cols, na.rm = na.rm, center = center,  : 
  Argument 'x' must be a matrix or a vector.

even

class(m3)
[1] "matrix"

[kashiff007]

Have you checked the first few lines of "m3" matrix. what is your head(m3) output?

[yusuf]

yes

> head(m3)

           geneid FP13w0L.x FP20w0L.x FP27w0L.x FP39w0R.x FP46w0R.x FP7w0L.x FP13w0L.y    
1: ENSG00000000003  5.832952  5.702980  5.890075  5.429769  6.197564 5.405774  6.093247    
2: ENSG00000000005  0.000000  4.092157  2.959349  2.626327  1.978803 2.133864  0.000000
3: ENSG00000000419  8.154151  7.716715  8.377897  8.100886  8.392561 8.289250  8.287379



   FP20w0L.y FP27w0L.y FP39w0R.y FP46w0R.y FP7w0L.y
1:  5.894538  6.105176  5.741960  6.249536 5.527603
2:  4.297580  3.116547  2.726263  2.077238 2.933729
3:  7.738360  8.420916  8.152382  8.435377 8.327208

[Corentin]

Can you try to do class(m3[,2:7]) ? sometimes the class of the object changes when you subset it.

If this is the case, then a solution to your problem would be plot(rowSds(as.matrix(m3[,2:7])), rowSds(as.matrix(m3[,8:13])))

[yusuf]

yup tried didn't work,

but made the matrix again and it worked.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Also, please do not use # in front of plain text content. If they're code comments, the entire content should be formatted as code.