trans_venn {microeco} | R Documentation |
This class is a wrapper for a series of venn analysis related methods, including venn result, 2- to 5-way venn diagram, more than 5-way petal plot and venn result transformations based on David et al. (2012) <doi:10.1128/AEM.01459-12>.
new()
trans_venn$new(dataset = NULL, sample_names = NULL, ratio = "numratio")
dataset
the object of microtable
Class.
sample_names
default NULL; if provided, filter the samples.
ratio
default numratio; NULL, "numratio" or "seqratio"; numratio: calculate number percentage; seqratio: calculate sequence percentage; NULL: no additional percentage.
venn_table venn_count_abund stored in trans_venn object.
data(dataset) t1 <- dataset$merge_samples(use_group = "Group") t1 <- trans_venn$new(dataset = t1, ratio = "numratio")
plot_venn()
Plot venn diagram.
trans_venn$plot_venn( color_circle = RColorBrewer::brewer.pal(8, "Dark2"), fill_color = TRUE, text_size = 4.5, text_name_size = 6, text_name_position = NULL, alpha = 0.3, linesize = 1.1, petal_plot = FALSE, petal_color = "skyblue", petal_a = 4, petal_r = 1, petal_use_lim = c(-12, 12), petal_center_size = 40, petal_move_xy = 4, petal_move_k = 2.3, petal_move_k_count = 1.3, petal_text_move = 40 )
color_circle
default RColorBrewer::brewer.pal(8, "Dark2"); color pallete
fill_color
default TRUE; whether fill the area color
text_size
default 4.5; text size in plot
text_name_size
default 6; name size in plot
text_name_position
default NULL; name position in plot
alpha
default .3; alpha for transparency
linesize
default 1.1; cycle line size
petal_plot
default FALSE; whether use petal plot.
petal_color
default "skyblue"; color of the petal
petal_a
default 4; the length of the ellipse
petal_r
default 1; scaling up the size of the ellipse
petal_use_lim
default c(-12, 12); the width of the plot
petal_center_size
default 40; petal center circle size
petal_move_xy
default 4; the distance of text to circle
petal_move_k
default 2.3; the distance of title to circle
petal_move_k_count
default 1.3; the distance of data text to circle
petal_text_move
default 40; the distance between two data text
ggplot.
t1$plot_venn()
trans_venn_com()
Transform venn result for the composition analysis.
trans_venn$trans_venn_com(use_OTUs_frequency = TRUE)
use_OTUs_frequency
default TRUE; whether only use OTUs occurrence frequency, i.e. presence/absence data; if FALSE, use abundance data.
a new microtable
class.
\donttest{ t2 <- t1$trans_venn_com(use_OTUs_frequency = TRUE) }
print()
Print the trans_venn object.
trans_venn$print()
clone()
The objects of this class are cloneable with this method.
trans_venn$clone(deep = FALSE)
deep
Whether to make a deep clone.
## ------------------------------------------------ ## Method `trans_venn$new` ## ------------------------------------------------ data(dataset) t1 <- dataset$merge_samples(use_group = "Group") t1 <- trans_venn$new(dataset = t1, ratio = "numratio") ## ------------------------------------------------ ## Method `trans_venn$plot_venn` ## ------------------------------------------------ t1$plot_venn() ## ------------------------------------------------ ## Method `trans_venn$trans_venn_com` ## ------------------------------------------------ t2 <- t1$trans_venn_com(use_OTUs_frequency = TRUE)