Enveomics collection

A toolbox for microbial genomics and metagenomics

Table.barplot.R

Creates nice barplots from tab-delimited tables.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

Table.barplot.R --x in_file [opts] out_file float float

§ Arguments

Input file*
 --x in_file  A tab-delimited file containing header (first row) and row names (first column).
Sizes
 --sizes string  A numeric vector containing the real size of the samples (columns) in the same order of the input table. If set, the values are assumed to be 100%, otherwise the sum of the columns is used. Separate values by commas.
Top
 --top integer  Maximum number of categories to display. Any additional categories will be listed as 'Others'.
Colors per group
 --colors-per-group integer  Number of categories in the first two saturation groups of colors. The third group contains the remaining categories if needed.
Bars width
 --bars-width integer  Width of the barplot with respect to the legend.
Legend ncol
 --legend-ncol integer  Number of columns in the legend.
Other col
 --other-col string  Color of the 'Others' category.
Add trend
 --add-trend   Controls if semi-transparent areas are to be plotted between the bars to connect the regions (trend regions).
Organic trend
 --organic-trend   Controls if the trend regions are to be smoothed (curves). By default, trend regions have straight edges. If TRUE, forces add.trend=TRUE.
Sort by
 --sort-by string  Any function that takes a numeric vector and returns a numeric scalar. This function is applied to each row, and the resulting values are used to sort the rows (decreasingly). Good options include: sd, min, max, mean, median.
Min report
 --min-report integer  Minimum percentage to report the value in the plot. Any value above 100 indicates that no values are to be reported.
Order
 --order string  Controls how the rows should be ordered. If empty (default), sort.by is applied per row and the results are sorted decreasingly. If NA, no sorting is performed, i.e., the original order is respected. If a vector is provided, it is assumed to be the custom order to be used (either by numeric index or by row names). Separate values by commas.
Col
 --col string  Colors to use. If provided, overrides the variables `top` and `colors.per.group`, but `other.col` is still used if the vector is insufficient for all the rows. Separate values by commas. An additional palette is available when using value 'coto' (palette contributed by Luis (Coto) Orellana).
Output file*
 out_file  Output file in PDF format.
width*
 float  Width of the plot (in inches).
height*
 float  Height of the plot (in inches).
* Mandatory.