convert matrix into dataframe in r

Question

I am trying to convert a matrix to a dataframe and use a column name and row name in the matrix with variables in the dataframe.
here is the sample

sample = matrix(c(1,NA,NA,2,NA,3,NA,NA,5,NA,NA,6,NA,NA,NA,NA,8,NA,3,1),ncol = 4)
colnames(sample) = letters[1:4]
row.names(sample) = letters[22:26]

My dataset has a lot of NA so I am trying to remove all the NA in the dataframe.

so here is my desiring output,

 data.frame(col = c("v","v","w","w","y","y","y","z"),
           row = c("a","b","c","c","a","b","d","d"), 
           value = c(1,3,6,8,2,5,3,1))

Answer 1

Use melt from reshape2 package for reshaping, then clear NA. Finally, do some formating stuff to get your desired output (ordering, setting colnames...).

> library(reshape2)
> df <- na.omit(melt(sample))  # reshaping
> df <- df[order(df$Var1), ]   # ordering
> colnames(df) <- c("col", "row", "value") # setting colnames
> df                           # getting desired output
   col row value
1    v   a     1
6    v   b     3
12   w   c     6
17   w   d     8
4    y   a     2
9    y   b     5
19   y   d     3
20   z   d     1

With dplyr and magrittr

> library(magrittr)
> library(dplyr)
> sample %>%  melt %>% 
    na.omit %>% 
    arrange(., Var1) %>%
    setNames(c('col', 'row', 'value'))

 col row value
1   v   a     1
2   v   b     3
3   w   c     6
4   w   d     8
5   y   a     2
6   y   b     5
7   y   d     3
8   z   d     1

Answer 2

Here is a base R method by replicating the row names and column names

out <- na.omit(data.frame(col = rownames(sample)[row(sample)],
     row = colnames(sample)[col(sample)], value = c(sample)))
out <- out[order(out$col),]
row.names(out) <- NULL
out
#  col row value
#1   v   a     1
#2   v   b     3
#3   w   c     6
#4   w   d     8
#5   y   a     2
#6   y   b     5
#7   y   d     3
#8   z   d     1