am_boxplot: am_boxplot object.

Description Usage Arguments Examples

View source: R/methods.R

Description

am_boxplot object.

Usage

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am_boxplot(x, cbPalette,
				alpha = 0.05,
				annot = c("none", "asterisks", "letters"),
				method = c("none","holm","hommel", "hochberg",
						   "bonferroni", "BH", "BY", "fdr"),
                  main = "Colonization", lab = "days", ...)

Arguments

x

dataset containing Trouvelot or Grid data

cbPalette

a vector of colors. Default is: c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7"). Colorbrewer and Colorgorical are website where is possible design nice color palettes.

alpha

Significant threshold

annot

Default is "none". If it is "asterisks" on the plot asterisks appear below the sample statistically different from the control. The control is the first sample in the input file. If is is "letters" on the plot letters appear below the samples groupping the samples based on the statistical test. For statistical tests check 'am_stat' function.

method

adjusts the p-value for multiple comparisons using the Bonferroni, Holm, Hochberg, Bonferroni, Benjamini-Hochberg, Benjamini-Yekutieli or fdr adjustment (see agricolae package for more details). The default is no adjustment for multiple comparisons.

main

Plot title. Default "Colonization".

lab

Parameter used in time series plots. It specified the label to write close the time on the plot. Default is "days".

...

ignored

Examples

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mchiapello/Ramf documentation built on Dec. 7, 2017, 7:48 a.m.