R one-liners for daily analysis

Here is a set of R one-liners that I use on a daily basis for my data analysis. See also the Stephen Turner's bioinformatics one-liners that gave me the inspiration. Note that the vast majority of the examples need the tidyverse library to be loaded. library(tidyverse).

Contents

• Working with matrix
• Reordering
• Colors
• Shiny
• Tidyr
• Dplyr
• Read a file
• R markdown

Matrix

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Use rownames as a column:

matrix %>% as.data.frame() %>% rownames_to_column("new_variable_name")

Matrix to long data frame

matrix %>% as.data.frame() %>% rownames_to_column("var1") %>% gather(var2, value, -1)

Matrix to heatmap

matrix %>% as.data.frame() %>% rownames_to_column("var1") %>% gather(var2, value, -1) %>% ggplot( aes(x=var1, y=var2)) + geom_tile()

Diagonal to NA

diag(matrix) <- NA

Reordering

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Reorder a factor using a specific order (forcats):

data %>% mutate( myfactor = fct_relevel( myfactor, "level1", "level2", "level3") )

Reorder a factor following the median of a numeric column (forcats):

data %>% mutate( myfactor = fct_reorder( myfactor, mynumeric, fun=median))

Other solution with dplyr:

data %>% arrange( mynumeric ) %>% mutate( myfactor = factor(myfactor, levels=myfactor)

Colors

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Shiny

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Tidyr

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Dplyr

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Rename columns:

data %>% rename(new_name=old_name, other_new_name=other_old_name)

Rename X by Y in a columns:

data %>% mutate( new = recode(old, X="Y") )

Replace by x in column 1 if column 2 as a certain value:

mtcars %>% mutate(mpg=replace(mpg, cyl==4, NA))

R markdown

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See the cheatsheet for basic tips.

Horizontal line to show a separation:

***

Center an image

<center>
![caption](/path/to/img)
</center>

Change background color of a specific part:

<style>
div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
</style>
<div class = "blue">
Add the text you want
</div>

Use buttons for secondary titles:

# Title 1  {.tabset .tabset-fade .tabset-pills}
## Title2

Show a data frame using the DT library:

datatable(data, rownames = FALSE, filter="top", options = list(pageLength = 5, scrollX=T) )

Add some white space to give some air in the document:

<br>

Format a number

A pvalue

A huge number

scales::comma(n)

On the axis of a ggplot

scale_y_comma