ggdiffclade {MicrobiotaProcess} | R Documentation |
plot results of different analysis or data.frame, contained hierarchical relationship or other classes,such like the tax_data of phyloseq.
ggdiffclade(obj, ...) ## S3 method for class 'data.frame' ggdiffclade( obj, nodedf, factorName, layout = "circular", linewd = 0.6, skpointsize = 0.8, alpha = 0.4, taxlevel = 6, cladetext = 2, factorLevels = NULL, setColors = TRUE, xlim = 12, reduce = FALSE, type = "species", ... ) ## S3 method for class 'diffAnalysisClass' ggdiffclade(obj, removeUnknown = TRUE, ...)
obj |
object, diffAnalysisClass, the results of diff_analysis
see also |
..., |
additional parameters. |
nodedf |
data.frame, contained the tax and the factor information and(or pvalue). |
factorName |
character, the names of factor in nodedf. |
layout |
character, the layout of ggtree, but only "rectangular", "radial", "slanted", "inward_circular" and "circular" in here, default is circular. |
linewd |
numeric, the size of segment of ggtree, default is 0.6. |
skpointsize |
numeric, the point size of skeleton of tree, default is 0.8 . |
alpha |
numeric, the alpha of clade, default is 0.4. |
taxlevel |
positive integer, the full text of clade, default is 5. |
cladetext |
numeric, the size of text of clade, default is 2. |
factorLevels |
list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this. |
setColors |
logical, whether set the color of clade, default is TRUE, or set FALSE,then use 'scale_fill_manual' setting. |
xlim |
numeric, the x limits, only works for 'inward_circular' layout, default is 12. |
reduce |
logical, whether remove the unassigned taxonomy, which will remove the clade of unassigned taxonomy, but the result of 'diff_analysis' should remove the unknown taxonomy, default is FALSE. |
type |
character, the type of datasets, default is "species", if the dataset is not about species, such as dataset of kegg function, you should set it to "others". |
removeUnknown |
logical, whether do not show unknown taxonomy, default is TRUE. |
figures of tax clade show the significant different feature.
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) #diffcladeplot <- ggdiffclade(diffres,alpha=0.3, linewd=0.2, # skpointsize=0.4, # taxlevel=3, # setColors=FALSE) + # scale_fill_manual(values=c('#00AED7', # '#FD9347', # '#C1E168'))