Create trans_venn object.
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$new( dataset = NULL, sample_names = NULL, ratio = NULL, add_abund_table = NULL )
datasetthe object of microtable Class.
sample_namesdefault NULL; if provided, filter the samples.
ratiodefault NULL; NULL, "numratio" or "seqratio"; numratio: calculate number percentage; seqratio: calculate sequence percentage; NULL: no additional percentage.
add_abund_tabledefault NULL; data.frame or matrix format; additional data provided instead of dataset$otu_table; Features must be rows.
data_details and data_summary stored in trans_venn object.
\donttest{
data(dataset)
t1 <- dataset$merge_samples(use_group = "Group")
t1 <- trans_venn$new(dataset = t1, ratio = "numratio")
}
plot_venn()
Plot venn diagram.
trans_venn$plot_venn( color_circle = RColorBrewer::brewer.pal(8, "Dark2"), fill_color = TRUE, text_size = 4.5, text_name_size = 6, text_name_position = NULL, alpha = 0.3, linesize = 1.1, petal_plot = FALSE, petal_color = "#BEAED4", petal_color_center = "#BEBADA", petal_a = 4, petal_r = 1, petal_use_lim = c(-12, 12), petal_center_size = 40, petal_move_xy = 4, petal_move_k = 2.3, petal_move_k_count = 1.3, petal_text_move = 40, other_text_show = NULL, other_text_position = c(2, 2), other_text_size = 5 )
color_circledefault RColorBrewer::brewer.pal(8, "Dark2"); color pallete
fill_colordefault TRUE; whether fill the area color
text_sizedefault 4.5; text size in plot
text_name_sizedefault 6; name size in plot
text_name_positiondefault NULL; name position in plot
alphadefault .3; alpha for transparency
linesizedefault 1.1; cycle line size
petal_plotdefault FALSE; whether use petal plot.
petal_colordefault "#BEAED4"; color of the petals.
petal_color_centerdefault "#BEBADA"; color of the center in the petal plot.
petal_adefault 4; the length of the ellipse
petal_rdefault 1; scaling up the size of the ellipse
petal_use_limdefault c(-12, 12); the width of the plot
petal_center_sizedefault 40; petal center circle size
petal_move_xydefault 4; the distance of text to circle
petal_move_kdefault 2.3; the distance of title to circle
petal_move_k_countdefault 1.3; the distance of data text to circle
petal_text_movedefault 40; the distance between two data text
other_text_showdefault NULL; other characters used to show in the plot
other_text_positiondefault c(1, 1); the text position for text in other_text_show
other_text_sizedefault 5; the text size for text in other_text_show
ggplot.
\donttest{
t1$plot_venn()
}
trans_comm()
Transform venn result to community-like microtable object for further composition analysis.
trans_venn$trans_comm(use_frequency = TRUE)
use_frequencydefault TRUE; whether only use OTUs occurrence frequency, i.e. presence/absence data; if FALSE, use abundance data.
a new microtable class.
\donttest{
t2 <- t1$trans_comm(use_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)
deepWhether 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_comm` ## ------------------------------------------------ t2 <- t1$trans_comm(use_frequency = TRUE)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.