ggbox {MicrobiotaProcess} | R Documentation |
A box or violin plot with significance test
ggbox(obj, factorNames, ...) ## S4 method for signature 'data.frame' ggbox( obj, sampleda, factorNames, indexNames, geom = "boxplot", factorLevels = NULL, compare = TRUE, testmethod = "wilcox.test", signifmap = FALSE, p_textsize = 2, step_increase = 0.1, boxwidth = 0.2, facetnrow = 1, controlgroup = NULL, comparelist = NULL, ... ) ## S4 method for signature 'alphasample' ggbox(obj, factorNames, ...)
obj |
object, alphasample or data.frame (row sample x column features). |
factorNames |
character, the names of factor contained in sampleda. |
... |
additional arguments, see also |
sampleda |
data.frame, sample information if obj is data.frame, the sampleda should be provided. |
indexNames |
character, the vector character, should be the names of features contained object. |
geom |
character, "boxplot" or "violin", default is "boxplot". |
factorLevels |
list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this. |
compare |
logical, whether test the features among groups,default is TRUE. |
testmethod |
character, the method of test, default is 'wilcox.test'.
see also |
signifmap |
logical, whether the pvalue are directly written a annotaion
or asterisks are used instead, default is (pvalue) FALSE. see also
|
p_textsize |
numeric, the size of text of pvalue or asterisks, default is 2. |
step_increase |
numeric, see also |
boxwidth |
numeric, the width of boxplot when the geom is 'violin', default is 0.2. |
facetnrow |
integer, the nrow of facet, default is 1. |
controlgroup |
character, the names of control group, if it was set, the other groups will compare to it, default is NULL. |
comparelist |
list, the list of vector, default is NULL. |
a 'ggplot' plot object, a box or violine plot.
Shuangbin Xu
## Not run: library(magrittr) otudafile <- system.file("extdata", "otu_tax_table.txt", package="MicrobiotaProcess") otuda <- read.table(otudafile, sep="\t", header=TRUE, row.names=1, check.names=FALSE, skip=1, comment.char="") samplefile <- system.file("extdata", "sample_info.txt", package="MicrobiotaProcess") sampleda <- read.table(samplefile, sep="\t", header=TRUE, row.names=1) otuda <- otuda[sapply(otuda, is.numeric)] %>% t() %>% data.frame(check.names=FALSE) set.seed(1024) alphaobj1 <- get_alphaindex(otuda, sampleda=sampleda) p1 <- ggbox(alphaobj1, factorNames="group") data(test_otu_data) test_otu_data %<>% as.phyloseq() set.seed(1024) alphaobj2 <- get_alphaindex(test_otu_data) class(alphaobj2) head(as.data.frame(alphaobj2)) p2 <- ggbox(alphaobj2, factorNames="group") # set factor levels. p3 <- ggbox(obj=alphaobj2, factorNames="group", factorLevels=list(group=c("M", "N", "B", "D"))) # set control group. p4 <- ggbox(obj=alphaobj2, factorNames="group", controlgroup="B") set comparelist p5 <- ggbox(obj=alphaobj2, factorNames="group", comparelist=list(c("B", "D"), c("B", "M"), c("B", "N"))) ## End(Not run)