am_dotplot2: am_dotplot2 object.

In mchiapello/Ramf: Arbuscular Mycorrhizal colonization calculation

am_dotplot2 object.

Description

am_dotplot2 object.

Usage

am_dotplot2(x, cbPalette,
				alpha = 0.05,
				annot = c("none", "asterisks", "letters"),
                 annot_size = 5,
				method = c("none","holm","hommel", "hochberg",
						   "bonferroni", "BH", "BY", "fdr"),
                  main = "Colonization", ...)

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.
annot_size	annotation font size. Default 5.
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".
...	ignored

Examples

am_dotplot2(example_grid)
am_dotplot2(example_trouvelot)

mchiapello/Ramf documentation built on April 9, 2022, 5:07 p.m.