How to plot scatter plot for a data in matrix form

I have data in a matrix form. I have two such matrices and want to plot it together for comparison purposes.

Type1:

  A B C D
A 1 2 3 4
B 2 1 7 8
C 3 7 1 9
D 4 8 9 1

Type2

  A  B  C  D
A 1  12 13 14
B 12 1  17 18
C 13 17 1  19
D 14 18 19 1

I want to keep type 1 as x-axis and type 2 as y-axis. How can I draw a scatter plot for this data using R?

Thanks a lot in advance!

You can first store your matrix values into a dataframe. You can use the function c(matrix1) to convert your matrix into a vector then storing this vector into a dataframe.

Then you can plot each dataframe new variable against each other.

### Import library
library(ggplot2)

### Simulating data
df <- data.frame(
  coordinate=c("AA", "AB", "AC", "AD", 
               "BA", "BB", "BC", "BD", 
               "CA", "CB", "CC", "CD",
               "DA", "DB", "DC", "DD"),
  matrix1=c(1, 2, 3, 4, 2, 1, 7, 8, 3, 7, 1, 9, 4, 8, 9, 1),
  matrix2=c(1, 12, 13, 14, 12, 1, 17, 18, 13, 17, 1, 19, 14, 18, 19, 1))

### Display plot
ggplot(data=df, aes(x=matrix1, y=matrix2)) + 
  geom_point()  + 
  geom_line() + 
  scale_x_continuous(limits=c(0, 20), breaks=seq(0, 20, 1)) + 
  scale_y_continuous(limits=c(0, 20), breaks=seq(0, 20, 1))

Sometimes it makes no sense to link the dots, if so, you can remove the geom_line() row.

Following your second question, if you want to add labels, you have many options. You can find two options with the following code, by either using geom_text_repel from ggrepel library or simply geom_text from ggplot2 library where you play with width and height arguments.

### Update group of labels with the same coordinates
df$matrixboth <- paste(df$matrix1, df$matrix2)

### Display plot
ggplot(data=df, aes(x=matrix1, y=matrix2, label=coordinate)) + 
  geom_point()  + 
  geom_line(color="#6aa6e7", size=1) + 
  scale_x_continuous(limits=c(0, 20), breaks=seq(0, 20, 1)) + 
  scale_y_continuous(limits=c(0, 20), breaks=seq(0, 20, 1)) + 
  # geom_text(position=position_jitter(width=0.6, height=0.6, aes(color=matrixboth)) + 
  ggrepel::geom_text_repel(aes(label=coordinate, color=matrixboth)) + 
  theme(legend.position="none")

geom_text_repel

geom_text