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rggplot2scatter-plotggpubr

In MDS with R, how to specify the scale?

In MDS with R, how shall I specify the scale that I want to use? For example, I want Dim.1 to have a scale of -80 to 60, and Dim.2 to have a scale of -70 to 30?

data("swiss")
head(swiss)
library(magrittr)
library(dplyr)
library(ggpubr)
# Cmpute MDS
mds <- swiss %>%
  dist() %>%          
  cmdscale() %>%
  as_tibble()
colnames(mds) <- c("Dim.1", "Dim.2")
# Plot MDS
ggscatter(mds, x = "Dim.1", y = "Dim.2", 
          label = rownames(swiss),
          size = 1,
          repel = TRUE)

mds plot

Source code taken from http://www.sthda.com/english/articles/31-principal-component-methods-in-r-practical-guide/122-multidimensional-scaling-essentials-algorithms-and-r-code/

Solution

  • You can change your scales' breaks by adding other ggplot2 arguments.

    data("swiss")
head(swiss)
#>              Fertility Agriculture Examination Education Catholic
#> Courtelary        80.2        17.0          15        12     9.96
#> Delemont          83.1        45.1           6         9    84.84
#> Franches-Mnt      92.5        39.7           5         5    93.40
#> Moutier           85.8        36.5          12         7    33.77
#> Neuveville        76.9        43.5          17        15     5.16
#> Porrentruy        76.1        35.3           9         7    90.57
#>              Infant.Mortality
#> Courtelary               22.2
#> Delemont                 22.2
#> Franches-Mnt             20.2
#> Moutier                  20.3
#> Neuveville               20.6
#> Porrentruy               26.6
library(magrittr)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(ggpubr)
#> Loading required package: ggplot2
# Cmpute MDS
mds <- swiss %>%
  dist() %>%          
  cmdscale() %>%
  as_tibble()
#> Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if
#> `.name_repair` is omitted as of tibble 2.0.0.
#> ℹ Using compatibility `.name_repair`.
colnames(mds) <- c("Dim.1", "Dim.2")
# Plot MDS
ggscatter(mds, x = "Dim.1", y = "Dim.2", 
          label = rownames(swiss),
          size = 1,
          repel = TRUE)+
  scale_y_continuous(breaks = seq(-70,30,20))+
  scale_x_continuous(breaks = seq(-80,60,20))
#> Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
#> increasing max.overlaps

    Created on 2023-01-07 with reprex v2.0.2