Heatmap of the most abundant bins

Generates a heatmap of the coverage profiles for the bins.

mmheatmap(mm, CLASSIFICATION = NULL, BIN_COL, TOPN = 20, tax_add = NULL)

Arguments

mm	(required) A dataframe loaded with mmload.
CLASSIFICATION	Name of the variable in mm with taxonomic classification. The format must resemble that of the following: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter;s__. (Default: NULL)
BIN_COL	(required) Group the scaffolds by a variable in mm.
TOPN	Number of the most abundant bins to display. (Default: 20)
tax_add	Taxonomic levels to show from the taxonomy variable, one of c("Kingdom","Phylum","Class","Order","Family","Genus","Species"). (Default: NULL)

Value

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

Author

Kasper Skytte Andersen ksa@bio.aau.dk

Rasmus Kirkegaard rhk@bio.aau.dk

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>
mmheatmap(
  mmgenome2,
  BIN_COL = "taxonomy",
  TOPN = 20
)
#> Warning: `select_()` was deprecated in dplyr 0.7.0.
#> Please use `select()` instead.
#> Warning: `group_by_()` was deprecated in dplyr 0.7.0.
#> Please use `group_by()` instead.
#> See vignette('programming') for more help
#> Warning: `rename_()` was deprecated in dplyr 0.7.0.
#> Please use `rename()` instead.
#> Selecting by mean_cov