ggeffectsize {MicrobiotaProcess} | R Documentation |
visualization of effect size by the Linear Discriminant Analysis or randomForest
ggeffectsize(obj, ...) ## S3 method for class 'data.frame' ggeffectsize( obj, factorName, effectsizename, factorLevels = NULL, linecolor = "grey50", linewidth = 0.4, lineheight = 0.2, pointsize = 1.5, setFacet = TRUE, ... ) ## S3 method for class 'diffAnalysisClass' ggeffectsize(obj, removeUnknown = TRUE, setFacet = TRUE, ...)
obj |
object, diffAnalysisClass see |
... |
additional arguments. |
factorName |
character, the column name contained group information in data.frame. |
effectsizename |
character, the column name contained effect size information. |
factorLevels |
list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this. |
linecolor |
character, the color of horizontal error bars, default is grey50. |
linewidth |
numeric, the width of horizontal error bars, default is 0.4. |
lineheight |
numeric, the height of horizontal error bars, default is 0.2. |
pointsize |
numeric, the size of points, default is 1.5. |
setFacet |
logical, whether use facet to plot, default is TRUE. |
removeUnknown |
logical, whether do not show unknown taxonomy, default is TRUE. |
the figures of effect size show the LDA or MDA (MeanDecreaseAccuracy).
Shuangbin Xu
## Not run: data(kostic2012crc) kostic2012crc %<>% as.phyloseq() 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) effectplot <- ggeffectsize(diffres) + scale_color_manual(values=c('#00AED7', '#FD9347', '#C1E168'))+ theme_bw()+ theme(strip.background=element_rect(fill=NA), panel.spacing = unit(0.2, "mm"), panel.grid=element_blank(), strip.text.y=element_blank()) ## End(Not run)