| ggdiffbox {MicrobiotaProcess} | R Documentation |
boxplot for the result of diff_analysis
ggdiffbox(obj, ...) ## S4 method for signature 'diffAnalysisClass' ggdiffbox( obj, geom = "boxplot", box_notch = TRUE, box_width = 0.05, dodge_width = 0.6, addLDA = TRUE, factorLevels = NULL, featurelist = NULL, removeUnkown = TRUE, colorlist = NULL, l_xlabtext = NULL, ... )
obj |
object, diffAnalysisClass class. |
..., |
additional arguments. |
geom |
character, "boxplot" or "violin", default is "boxplot". |
box_notch |
logical, see also 'notch' of |
box_width |
numeric, the width of boxplot, default is 0.05 |
dodge_width |
numeric, the width of dodge of boxplot, default is 0.6. |
addLDA |
logical, whether add the plot to visulize the result of LDA, default is TRUE. |
factorLevels |
list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this. |
featurelist |
vector, the character vector, the sub feature of originalD in diffAnalysisClass,default is NULL. |
removeUnkown |
logical, whether remove the unknow taxonomy, default is TRUE. |
colorlist |
character, the color vector, default is NULL. |
l_xlabtext |
character, the x axis text of left panel, default is NULL. |
a 'ggplot' plot object, a box or violine plot for the result of diffAnalysisClass.
Shuangbin Xu
data(kostic2012crc)
kostic2012crc
head(phyloseq::sample_data(kostic2012crc),3)
kostic2012crc <- phyloseq::rarefy_even_depth(kostic2012crc,
rngseed=1024)
table(phyloseq::sample_data(kostic2012crc)$DIAGNOSIS)
set.seed(1024)
diffres <- diff_analysis(kostic2012crc, classgroup="DIAGNOSIS",
mlfun="lda", filtermod="fdr",
firstcomfun = "kruskal.test",
firstalpha=0.05, strictmod=TRUE,
secondcomfun = "wilcox.test",
subclmin=3, subclwilc=TRUE,
secondalpha=0.01, ldascore=3)
library(ggplot2)
p <- ggdiffbox(diffres, box_notch=FALSE, l_xlabtext="relative abundance")
# set factor levels
#p2 <- ggdiffbox(diffres, box_notch=FALSE, l_xlabtext="relative abundance",
# factorLevels=list(DIAGNOSIS=c("Tumor", "Healthy")))