pcoa_plot {mina} | R Documentation |
Visulization of components distance / dissimilarity in k dimension.
Visulization of components distance / dissimilarity in k dimension.
pcoa_plot(x, des, match, ...) ## S4 method for signature 'list,data.frame,character' pcoa_plot(x, des, match, d1 = 1, d2 = 2, color, shape = NULL, ...)
x |
A list generated by 'dmr'. |
des |
The corresponding descriptive table. |
match |
The column name of the components IDs in 'des' with exactly the same as rownames in x. |
... |
Additional parameters. |
d1 |
The dimension be visualized in x-axis, default '1'. |
d2 |
The dimension be visualized in y-axis, default '2'. |
color |
The column name in 'des' to be used for different color groups. |
shape |
The column name in 'des' to be used for different shape groups, default 'NULL'. |
p The plotted figure.
p The plotted PCoA.
maize <- new("mina", tab = maize_asv2, des = maize_des2) maize <- norm_tab(maize, method = "raref") maize <- fit_tabs(maize) maize <- com_dis(maize, method = "bray") maize <- dmr(maize) asv_dmr <- .dmr(maize) des <- des(maize) p1a <- pcoa_plot(asv_dmr, des, match = "Sample_ID", color = "Compartment") p1b <- pcoa_plot(asv_dmr, des, match = "Sample_ID", d1 = 3, d2 = 4, color = "Compartment") p2a <- pcoa_plot(asv_dmr, des, match = "Sample_ID", color = "Host_genotype") p2b <- pcoa_plot(asv_dmr, des, match = "Sample_ID", d1 = 1, d2 = 3, color = "Host_genotype") p3a <- pcoa_plot(asv_dmr, des, match = "Sample_ID", color = "Compartment", shape = "Soil") p3b <- pcoa_plot(asv_dmr, des, match = "Sample_ID", d1 = 1, d2 = 4, color = "Compartment", shape = "Soil") maize <- new("mina", tab = maize_asv2, des = maize_des2) maize <- norm_tab(maize, method = "raref") maize <- fit_tabs(maize) maize <- com_dis(maize, method = "bray") maize <- dmr(maize) asv_dmr <- .dmr(maize) des <- des(maize) p1a <- pcoa_plot(asv_dmr, des, match = "Sample_ID", color = "Compartment") p1b <- pcoa_plot(asv_dmr, des, match = "Sample_ID", d1 = 3, d2 = 4, color = "Compartment") p2a <- pcoa_plot(asv_dmr, des, match = "Sample_ID", color = "Host_genotype") p2b <- pcoa_plot(asv_dmr, des, match = "Sample_ID", d1 = 1, d2 = 3, color = "Host_genotype") p3a <- pcoa_plot(asv_dmr, des, match = "Sample_ID", color = "Compartment", shape = "Soil") p3b <- pcoa_plot(asv_dmr, des, match = "Sample_ID", d1 = 1, d2 = 4, color = "Compartment", shape = "Soil")