ggdifftaxbar {MicrobiotaProcess} | R Documentation |
significantly discriminative feature barplot
ggdifftaxbar(obj, ...) ggdiffbartaxa(obj, ...) ## S4 method for signature 'diffAnalysisClass' ggdifftaxbar( obj, filepath = NULL, output = "biomarker_barplot", removeUnknown = TRUE, figwidth = 6, figheight = 3, ylabel = "relative abundance", format = "pdf", dpi = 300, ... ) ## S3 method for class 'featureMeanMedian' ggdifftaxbar( obj, featurename, classgroup, subclass, xtextsize = 3, factorLevels = NULL, coloslist = NULL, ylabel = "relative abundance", ... )
obj |
object, diffAnalysisClass see also
|
... |
additional arguments. |
filepath |
character, default is NULL, meaning current path. |
output |
character, the output dir name, default is "biomarker_barplot". |
removeUnknown |
logical, whether do not show unknown taxonomy, default is TRUE. |
figwidth |
numeric, the width of figures, default is 6. |
figheight |
numeric, the height of figures, default is 3. |
ylabel |
character, the label of y, default is 'relative abundance'. |
format |
character, the format of figure, default is pdf, png, tiff also be supported. |
dpi |
numeric, the dpi of output, default is 300. |
featurename |
character, the feature name, contained at the objet. |
classgroup |
character, factor name. |
subclass |
character, factor name. |
xtextsize |
numeric, the size of axis x label, default is 3. |
factorLevels |
list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this. |
coloslist |
vector, color vector, if the input is phyloseq, you should use this to adjust the color, not scale_color_manual. |
the figures of features show the distributions in samples.
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) # not run in example #ggdifftaxbar(diffres, output="biomarker_barplot")