Function reference • pcutils

Little tools A collection of little tools for analysis
`lib_ps()`	Attach packages or install packages have not benn installed
`del_ps()`	Detach packages
`dabiao()`	Print some message with =
`copy_vector()`	Copy a vector
`copy_df()`	Copy a data.frame
`change_fac_lev()`	Change factor levels
`tidai()`	Replace a vector by named vector
`update_param()`	Update the parameters
`sanxian()`	Three-line table
`grepl.data.frame()`	Grepl applied on a data.frame
`gsub.data.frame()`	Gsub applied on a data.frame
`read.file()`	Read some special format file
`trans_format()`	Transfer the format of file
`read_fasta()`	Read fasta file
`write_fasta()`	Write a data.frame to fasta
`download2()`	Download File
`search_browse()`	Search and browse the web for specified terms
`translator()`	Translator
`download_ncbi_genome_file()`	Download genome files from NCBI based on accession number
Statistics A collection of statistical tools
`remove.outliers()`	Remove outliers
`count2()`	Like `uniq -c` in shell to count a vector
`hebing()`	Group your data
`guolv()`	Filter your data
`rm_low()`	Remove the low relative items in each column
`trans()`	Trans format your data
`mmscale()`	Min_Max scale
`strsplit2()`	Split Composite Names
`t2()`	Transpose data.frame
`explode()`	Explode a data.frame if there are split charter in one column
`squash()`	Squash one column in a data.frame using other columns as id.
`match_df()`	Match otutab and metadata
`df2distance()`	Convert Three-column Data to Distance Matrix
`df2link()`	df to link table
`pre_number_str()`	Prepare a numeric string
`split_text()`	Split text into parts, each not exceeding a specified character count
`twotest()`	Two-group test
`multitest()`	Multi-groups test
`group_test()`	Performs multiple mean comparisons for a data.frame
`fittest()`	Fit a distribution
`toXY()`	Transfer Geographical latitude and longitude to XY(m)
`lm_coefficients()`	Get coefficients of linear regression model
`plot(<coefficients>)`	Plot coefficients as a bar chart or lollipop chart
`multireg()`	Multiple regression/ variance decomposition analysis
Visualization A collection of visualization tools
`rgb2code()`	Transform a rgb vector to a Rcolor code
`is.ggplot.color()`	Judge if a characteristic is Rcolor
`add_alpha()`	Add alpha for a Rcolor
`plotpdf()`	Plot a multi-pages pdf
`plotgif()`	Plot a gif
`get_cols()`	Get n colors
`scale_fill_pc()`	Scale a fill color
`scale_color_pc()`	Scale a fill color
`add_theme()`	Add a global gg_theme and colors for plots
`legend_size()`	Scale a legend size
`ggplot_lim()`	Get a ggplot xlim and ylim
`generate_labels()`	Generate labels position
`ggplot_translator()`	Translate axis label of a ggplot
`stackplot()` `areaplot()`	Plot a stack plot
`cor_plot()`	Plot correlation
`group_box()`	Plot a boxplot
`gghuan()`	Plot a doughnut chart
`gghuan2()`	gghuan2 for multi-doughnut chart
`my_lm()`	Fit a linear model and plot
`china_map()`	Plot china map
`sample_map()`	Plot the sampling map
`gghist()`	gg histogram
`ggheatmap()`	Heatmap by ggplot
`ggmosaic()`	ggmosaic for mosaic plot
`venn()`	Plot a general venn (upset, flower)
`tax_pie()`	Pie plot
`tax_radar()`	Radar plot
`my_sankey()`	My Sankey plot
`my_circo()`	My circo plot
`my_sunburst()`	My Sunburst plot
`my_treemap()`	My Treemap plot
`my_voronoi_treemap()`	My Voronoi treemap plot
`my_circle_packing()`	My Circle packing plot
Project A collection of project tools
`make_project()`	Make a R-analysis project
`add_analysis()`	Add an analysis for a project
`make_gitbook()`	Make a Gitbook using bookdown
`how_to_set_font_for_plot()`	How to set font for ggplot
`how_to_set_options()`	How to set options in a package
`how_to_update_parameters()`	How to update parameters
`how_to_use_parallel()`	How to use parallel
`how_to_use_sbatch()`	How to use sbatch
`prepare_package()`	Prepare a package
`update_NEWS_md()`	Update the NEW.md for a package
`set_pcutils_config()`	Set config
`show_pcutils_config()`	Show config
`my_cat()`	Show my little cat named Guo Dong which drawn by my girlfriend.
Data A collection of data
`otutab`	test data for pcutils package
`metadata`	test data for pcutils package
`taxonomy`	test data for pcutils package
`little_guodong`	My cat

Reference

Little tools

Statistics

Visualization

Project

Data