enve.barplot {enveomics.R}

Enveomics: Barplot

Description

Creates nice barplots from tab-delimited tables.

Usage

enve.barplot(
  x,
  sizes,
  top = 25,
  colors.per.group = 9,
  bars.width = 4,
  legend.ncol = 1,
  other.col = "#000000",
  add.trend = FALSE,
  organic.trend = FALSE,
  sort.by = median,
  min.report = 101,
  order = NULL,
  col,
  ...
)

Arguments

x

Can be either the input data or the path to the file containing the table.

• If it contains the data, it must be a data frame or an object coercible to a data frame.

• If it is a path, it must point to a tab-delimited file containing a header (first row) and row names (first column).

sizes

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.

top

Maximum number of categories to display. Any additional categories will be listed as "Others".

colors.per.group

Number of categories in the first two saturation groups of colors. The third group contains the remaining categories if needed.

bars.width

Width of the barplot with respect to the legend.

legend.ncol

Number of columns in the legend.

other.col

Color of the "Others" category.

add.trend

Controls if semi-transparent areas are to be plotted between the bars to connect the regions (trend regions).

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

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

Minimum percentage to report the value in the plot. Any value above 100 indicates that no values are to be reported.

order

Controls how the rows should be ordered.

• If NULL (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).

col

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. An additional palette is available with col='coto' (contributed by Luis (Coto) Orellana).

...

Any additional parameters to be passed to barplot.

Value

No return value

Author(s)

Luis M. Rodriguez-R [aut, cre]

Examples

# Load data
data("phyla.counts", package = "enveomics.R", envir = environment())
# Create a barplot sorted by variance with organic trends
enve.barplot(
  phyla.counts, # Counts of phyla in four sites
  sizes = c(250,100,75,200), # Total sizes of the datasets of each site
  bars.width = 2, # Decrease from default, so the names are fully displayed
  organic.trend = TRUE, # Nice curvy background
  sort.by = var # Sort by variance across sites
)