humann2Barplot.RdGenerates barplots statified by taxon and metadata for one HUMAnN2 feature, similar to `humann2_barplot` Optimized for viewability of many features in one figure by limiting the number of statifications.
humann2Barplot( humann2.table, num.bugs = "auto", num.bugs.explained.fraction = 0.25, feature = "Cas1", featue.column = 1, taxa.column = 2, metadata, metadata.id = 9, metadata.factor = 4, use.custom.column.stratification = T, order.by = "bc", column.stratification.order = c("Oral", "Skin", "Vaginal", "Gut"), custom.order, last.plot.colors = NULL )
| humann2.table | a dataframe containing the HUMAnN2 output in tsv format |
|---|---|
| num.bugs | number of most abundant bugs to show as statification, set to to "auto" if this should be ajusted based on num.bugs.explained.fraction |
| num.bugs.explained.fraction | fraction that needs to be explained by the number of bugs shown |
| feature | name of gene in humann2_table that will be plotted |
| featue.column | index of column in humann2 table that holds the feature |
| taxa.column | index of column in humann2 table that holds the taxon infomation |
| metadata | a dataframe containing the metadata |
| metadata.id | column in metadata file that holds the smaple id (colum names in humann2 table) |
| metadata.factor | column in metadata file that holds the annotation of interest |
| use.custom.column.stratification | custom orderin of row statification |
| order.by | how to order bars within one statification |
| column.stratification.order | oder of entries in metadata.factor |
| custom.order | custom sample order |
| last.plot.colors | dataframe of plot colors for additional cross-lookup of taxa information |