R_stuff

01 mean 02 spearman

07. hist vs ggplot2 geom_histogram

see https://www.jianshu.com/p/16e2022c025d

data = read.csv("C:\\Users\\cy006\\Desktop\\01.R_test.csv", header=T)

ID = c(0,1,2,3,4,5)

Gender = c('male','female','male','female','male','female')

Height = c(178,156,170,158,168,155)

次数直方图或频数直方图，

hist(Height,freq = T)

频率直方图

hist(Height,freq = F)
NO.5
install.packages("ggplot2")
library(ggplot2)

ggplot(data, aes(x=Height, y=..count..  )) + geom_histogram(stat="bin", binwidth = 4, colour="black", fill="white")
ggplot(data, aes(x=Height, y=..density..)) + geom_histogram(stat="bin", binwidth = 4, colour="black", fill="white")

R_Graphics_Cookbook.R

is a book note of the "R Graphics Cookbook", learning ...

ggplot violin graph

igblast.result.visualization.R

for example

Rscript igblast.result.visualization.R
# may generate a pdf file with violin plot.

R Graphics Cookbook learning

R_Graphics_Cookbook.2.R is a note book.

Venn diagram

see: https://www.jianshu.com/p/05f4bae28443 Rscript venn.R <file1> <file2> ...

basic boxplot

Rscript ggplot_boxplot_basic.R <file>

geom_boxplot

Rscript geom_boxplot.R <boxplot.data.txt> ...

correlation.R

there are two scripts to draw correlation graph. correlation.point.R correlation.point.log.R

correlation.R

new correlation plot:

suitable for PPT, log scale, scientific axis lable.

EnrichmentAnalysis

GO enrichment and KEGG enrichment analysis examples

Clustering Analysis practice

hierarchical clustering example 1:https://www.jianshu.com/p/f2413cdfd4f0
hierarchical clustering example 2:https://www.jianshu.com/p/4131fbf8cd3e
hierarchical clustering example 3:https://www.jianshu.com/p/60c490fe2a1f
K-means clustering example 1:https://www.jianshu.com/p/dfc6f9b13256
K-means clustering example 2:https://www.jianshu.com/p/eb9d6e9670c5

10X Genomics RNA-seq analysis