Some Useful Functions for Statistics and Visualization

Offers a range of utilities and functions for everyday programming tasks. 1.Data Manipulation. Such as grouping and merging, column splitting, and character expansion. 2.File Handling. Read and convert files in popular formats. 3.Plotting Assistance. Helpful utilities for generating color palettes, validating color formats, and adding transparency. 4.Statistical Analysis. Includes functions for pairwise comparisons and multiple testing corrections, enabling perform statistical analyses with ease. 5.Graph Plotting, Provides efficient tools for creating doughnut plot and multi-layered doughnut plot; Venn diagrams, including traditional Venn diagrams, upset plots, and flower plots; Simplified functions for creating stacked bar plots, or a box plot with alphabets group for multiple comparison group.

pcutils

pcutils is a package that contains some useful functions for me, it offers a range of utilities and functions for everyday programming tasks.

The HTML documentation of the latest version is available at Github page.

Installation

The stable version is available on CRAN:

install.packages("pcutils")

Or you can install the development version of pcutils from GitHub with:

# install.packages("devtools")
devtools::install_github("Asa12138/pcutils")

Little tools

• lib_ps, del_ps can library or detach packages gracefully

• dabiao print a message dabiao("Message",char = "😀",n = 20): 😀😀😀😀😀😀Message😀😀😀😀😀😀

• copy_vector help to copy a vector, like datapasta package; copy_df help to copy a dataframe

• change_fac_lev can change a factor levels; tidai can replace a vector by named vector

• update_param update a parameter in a function

• sanxian print a three-line table

• grepl.data.frame and gsub.data.frame do grepl and gsub on a dataframe.

for file

• read.file read some special format files

• trans_format convert file format like jpg, png, svg, pdf, html…

• read_fasta and write_fasta read and write fasta file

for web

• download2 download a file from a url

• download_ncbi_genome_file download a file from NCBI

• search_browse search and browse a website

• translator translate a text

Statistics

data preprocessing

• remove.outliers remove the outliers

• count2 imitate the uniq -c in shell

• hebing group your dataframe; guolv filter a dataframe; rm_low remove low frequency

• trans transfer your data

• mmscale do a scale specifying the min and max

• strsplit2 is better than strsplit for me; t2 is better than t for me

• explode expand a column in dataframe; squash squash a dataframe

• pre_number_str prepare a number string

statistical test

• twotest do a two-group test and multitest do a multi-group test; group_test performs multiple mean comparisons for a data.frame

• fittest test a vector fit which distribution

• toXY transfer geographical latitude and longitude to XY(m)

• lm_coefficients get the coefficients of a linear model; multireg fit a multiple linear model

Visualization

utils for plot

• rgb2code convert between r,g,b and color code; is.ggplot.color judge a right color; add_alpha add a alpha for a color

• plotpdf, plotgif print pdf or gif for a plot list

• get_cols generate n colors based on a palette; scale_fill_pc and scale_color_pc are scales for ggplot

• add_theme generate a mytheme object for ggplot

• legend_size resize the legend for a ggplot; ggplot_lim get the x-y limits for a ggplot

• generate_labels generate points position for a series of labels

• ggplot_translator translate the text of a ggplot

plot functions

• stackplot plot a bar plot or stack bar plot easily; areaplot plot a area plot easily

• my_sankey plot a sankey plot

• cor_plot plot a correlation plot

• group_box plot a boxplot easily

• gghuan plot a doughnut chart; gghuan2 plot a multi-doughnut chart

• my_lm fit a linear model and plot

• china_map plot a china map; sample_map plot a sample map

• gghist plot a histogram

• venn plot a venn plot

• tax_pie plot a pie plot

• tax_radar plot a radar plot

• my_circo plot a circlize plot

• my_sunburst plot a sunburst plot

• my_circle_packing plot a circle packing plot

• my_treemap plot a treemap plot

• my_voronoi_treemap plot a voronoi treemap plot

Project

• make_project build a R project

• add_analysis create a specific Rmd file

• make_gitbook build a git book

Package

• prepare_package prepare a package

• update_NEWS_md update the NEWS.md

Easter Egg： my_cat will show my little cat named GuoDong.