Plot multiple combinations of variables in a pairs plot

Plots multiple variables from the given mm object in a grid plot with all pairs of variables using mmplot.

mmplot_pairs(mm, variables = NULL, textsize = 5, axis_ticks = TRUE, ...)

Arguments

mm	(required) A dataframe loaded with mmload.
variables	A vector of 3 or more variable names in mm to plot on each axis. If NULL, the default, then all coverage variables will be plotted as well as GC content. (Default: NULL)
textsize	The text size of the axis titles. (Default: 5)
axis_ticks	Hide or show axis ticks on both axes. (Default: TRUE)
...	Arguments passed on to mmplot, eg. color_by, min_length, axis scales and more, see help("mmplot").

Value

A ggplot object. Note that mmgenome2 hides all warnings produced by ggplot objects.

Author

Kasper Skytte Andersen ksa@bio.aau.dk

Soren M. Karst smk@bio.aau.dk

Mads Albertsen MadsAlbertsen85@gmail.com

Examples

library(mmgenome2)
data(mmgenome2)
mmgenome2
#> # A tibble: 97,285 x 13
#>    scaffold length    gc cov_C13.11.14 cov_C13.11.25 cov_C13.12.03 cov_C14.01.09
#>    <chr>     <dbl> <dbl>         <dbl>         <dbl>         <dbl>         <dbl>
#>  1 1          8264  57.8       1.44             53.6         0             0.066
#>  2 2          1027  57.0       0.625            24.2         0             0    
#>  3 3          1665  55.9      13.5             434.          0.166         0.177
#>  4 4          9056  35.9       0.01             23.4         0             0    
#>  5 5          3343  64.0       3.20             16.4         0             0    
#>  6 6         98207  39.1       0.00966          24.5         3.29          9.85 
#>  7 7          6480  63.0       2.61             19.2         1.46         12.3  
#>  8 8         15790  61.7       2.78             21.2         1.62         10.3  
#>  9 9          1403  70.4      85.1             192.          0             0    
#> 10 10         2018  70.2      50.3             101.          0             0    
#> # … with 97,275 more rows, and 6 more variables: PC1 <dbl>, PC2 <dbl>,
#> #   PC3 <dbl>, geneID <chr>, taxonomy <fct>, rRNA16S <fct>
mmplot_pairs(mmgenome2,
  variables = c("cov_C13.11.14", "cov_C13.11.25", "cov_C13.12.03", "cov_C14.01.09"),
  min_length = 10000,
  color_by = "taxonomy",
  x_scale = "log10",
  y_scale = "log10",
  x_limits = c(1, NA),
  y_limits = c(1, NA)
)