Statistical Visualization Tools

Visualization functions in the applications of translational medicine (TM) and biomarker (BM) development to compare groups by statistically visualizing data and/or results of analyses, such as visualizing data by displaying in one figure different groups' histograms, boxplots, densities, scatter plots, error-bar plots, or trajectory plots, by displaying scatter plots of top principal components or dendrograms with data points colored based on group information, or visualizing volcano plots to check the results of whole genome analyses for gene differential expression.


v1.0.9 created on April 10, 2019 (1) modify XYscatter. all plots have the same x-axis and y-axis range (2) set delta = 0.2 (instead of 0.5) in BiAxisErrBar

v1.0.8 created on April 5, 2019 (1) fixed a bug in 'BiAxisErrBar': no line connect means

v1.0.7 created on April 4, 2019 (1) before set 'x' or 'group' as factor, first test if they are already factor v1.0.6 created on April 3, 2019 and modified on April 4, 2019 (1) fixed a bug in 'Box' function: added "+ scale_x_discrete(drop = F) + scale_fill_discrete(drop = F) +" (2) set default value for jitter.width=1 and point.size = 1 (3) in 'PCA_score', add the input 'title' (4) in 'PCA_score', if 'color' not NULL, then set data[, c(color)]=as.factor(data[, c(color)]) (5) added "+ xlab(label=xlab) + ylab(label=ylab)" to functions 'BoxROC', 'XYscatter', 'PVCA', and 'ImpPlot' (6) fixed a bug in 'XYscatter', 'Hist', and 'Den': when 'group=NULL', there is an error (7) in 'Heat', replace 'heatmap.2' by 'pheatmap' (8) in 'LinePlot' and 'Box', set 'x' and 'group' as factor (9) in 'BiAxisErrBar', set 'x' as factor

v1.0.5 created on Mar. 12, 2019 (1) revised DESCRIPTION file based on CRAN's comments: Please omit the redundant "We provide novel..." and start your description with "Visualization functions ...". Please explain all acronyms (e.g. PCA) in your Description field to avoid misunderstandings.

v1.0.4 created on Mar. 7, 2019 (1) revised back Dependency to R 3.5.0 since Writting R extension document mentions that "It is inadvisable to use a dependence on R with patchlevel (the third digit) other than zero. Doing so with packages which others depend on will cause the other packages to become unusable under earlier versions in the series, and e.g. versions 3.x.1 are widely used throughout the Northern Hemisphere academic year."

v1.0.3 created on Mar. 7, 2019 (1) Dependency R 3.5.2 v1.0.2 created on Mar. 7, 2019 (1) The warning "'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN " is caused by the loading of 'ggplot2' package. Try to increase R dependency to R3.5.1 to solve this problem v1.0.1 created on Mar. 7, 2019 (1) fixed 1 warning and 2 notes reported by CRAN teams' auto-check service (2) deleted unused functions and comments in R files v1.0.0 created on Feb. 19, 2019 (1) ready for submission

Reference manual

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1.2.1 by Wenfei Zhang, a year ago

Browse source code at

Authors: Wenfei Zhang [aut, cre] , Weiliang Qiu [aut, ctb] , Xuan Lin [aut, ctb] , Donghui Zhang [aut, ctb]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports GGally, dplyr, reshape2, ggdendro, tibble, ggfortify, ggrepel, gbm, forestplot, rpart.plot, grDevices, gridExtra, pROC, factoextra, methods, pvca, limma, randomForest, glmnet, knitr, rmarkdown, pheatmap, RColorBrewer, graphics, tidyverse, magrittr

Depends on Biobase, ggplot2, stats

See at CRAN