am_dotplot.Rd
am_dotplot object.
am_dotplot(x, cbPalette, alpha = 0.05, annot = c("none", "asterisks", "letters"), annot_size = 5, method = c("none","holm","hommel", "hochberg", "bonferroni", "BH", "BY", "fdr"), legend = c("right", "left", "top", "bottom"), main = "Gridline intersect method", ...)
x | dataset containing Trouvelot or Grid data |
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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. |
legend | Indicate the legend position |
main | Plot title. Default "Colonization". |
... | ignored |
am_dotplot(example_grid)am_dotplot(example_trouvelot)