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rmatrixplotscatter-plotvegan

R: Plot data in matrix against data from one column

I have a matrix containing >200 data points. This is my object x. In a second object (metadata), I have a column (y) with 20 data points. I would like to plot the matrix (object x) against the 20 data points (y) in object metadata

plot(x, metadata$y)

does not work, as x and y lengths differ. Is it possible to plot this?

Matrix x:

    X1  X4  X7  X9
X4  0.7                                                            
X7  0.8 0.5                                                  
X9  0.6 0.6 0.7

metadata

X1 65.4
X4 9.7
X7 47.4
X9 14.5

metadata$y: 65.4 9.7 47.4 14.5

Solution

  • Here's a tidyverse solution: Alright, with these data frames (structure at bottom of post):

    > df
    X1  X4  X7 X9
X4 0.7  NA  NA NA
X7 0.8 0.5  NA NA
X9 0.6 0.6 0.7 NA

> metadata
      y
X1 65.4
X4  9.7
X7 47.4
X9 14.5

    First, pull the rownames() from metadata for simplicity:

    metadata$x <- rownames(metadata)

> metadata
      y  x
X1 65.4 X1
X4  9.7 X4
X7 47.4 X7
X9 14.5 X9

    Now use gather to convert the x matrix into a long format dataframe, using 'x' as the key, just as exists the rownames step above. Next, use left_join to join the metadata to the long dataframe, using the x in both dataframes as the common column.

    long <- gather(df, key = "x") %>%
  left_join(metadata, by = "x")

> long
    x value    y
1  X1   0.7 65.4
2  X1   0.8 65.4
3  X1   0.6 65.4
4  X4    NA  9.7
5  X4   0.5  9.7
6  X4   0.6  9.7
7  X7    NA 47.4
8  X7    NA 47.4
9  X7   0.7 47.4
10 X9    NA 14.5
11 X9    NA 14.5
12 X9    NA 14.5

    Plot:

    plot(value ~ y, data = long, pch = 19)

    enter image description here

    Data:

    df <-
  structure(
    list(
      X1 = c(0.7, 0.8, 0.6),
      X4 = c(NA, 0.5, 0.6),
      X7 = c(NA,
             NA, 0.7),
      X9 = c(NA, NA, NA)
    ),
    .Names = c("X1", "X4", "X7", "X9"),
    row.names = c("X4", "X7", "X9"),
    class = "data.frame"
  )

metadata <-
  structure(
    list(y = c(65.4, 9.7, 47.4, 14.5)),
    .Names = "y",
    row.names = c("X1",
                  "X4", "X7", "X9"),
    class = "data.frame"
  )