This tools prepare boxplot and dotplot from the cell biology experimental data.
gamma H2AX foci or any other foci number upon any drug treatment can be visualized by this tool.
This is just a command line implementation of ggpubR package,
which itself is based on the infamous ggplot2, by Hadley Wickham,.
The tool has some library dependancies.
- The easiest way to get ggplot2 is to install the whole tidyverse:
install.packages("tidyverse")Alternatively, install just ggplot2:
install.packages("ggplot2")- Install from CRAN as follow:
install.packages("ggpubr")- Or, install the latest version from GitHub as follow:
if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggpubr")- To install the latest version released on CRAN use the following command:
install.packages("argparse")- The easiest way to get ggplot2 is to install the whole tidyverse:
install.packages("tidyverse")- Alternatively, install just tidyr:
install.packages("tidyr")- The easiest way to get magrittr is to install the whole tidyverse:
install.packages("tidyverse")- Alternatively, install just magrittr:
install.packages("magrittr")- Get the released version from cran
install.packages("reshape2")- The easiest way to install the latest released version from CRAN is to install the whole tidyverse.
install.packages("tidyverse")- Alternatively, install just readxl from CRAN:
install.packages("readxl")$ Rscript --vanilla boxplotter_cli.R -h
usage: boxplotter_cli.R [-h] [--file FILE [FILE ...]] [--x-ax X_AX]
[--y-ax Y_AX] [--reorder REORDER [REORDER ...]]
[--color COLOR] [--fill FILL] [--alpha ALPHA]
[--palette PALETTE [PALETTE ...]] [--facet FACET]
[--facet-col FACET_COL] [--x-lab X_LAB]
[--y-lab Y_LAB] [--title TITLE] [--dot DOT]
[--dot-color DOT_COLOR] [--dot-fill DOT_FILL]
[--dot-alpha DOT_ALPHA] [--dot-size DOT_SIZE]
[--dot-val DOT_VAL] [--out OUT]
[--fig-size FIG_SIZE FIG_SIZE] [--show-outliers]
[--stat] [--stat-method STAT_METHOD]
[--stat-comp STAT_COMP [STAT_COMP ...]]
[--stat-pos STAT_POS [STAT_POS ...]] [--yscale YSCALE]
[--max-y MAX_Y] [--xtick-angle XTICK_ANGLE]
[--legend LEGEND] [--hide-ticks]
DESCRIPTION
BoxPlotteR
Tools for making plot from command line
For more color option option visit
https://github.com/paulahsan/boxplotteR/blob/master/ggplot2-colour-names.png
or https://jaredhuling.org/jcolors/
optional arguments:
-h, --help show this help message and exit
Data parser: parse the data file and axis related arguments:
--file FILE [FILE ...]
Input file name. Can read csv and excel file.
For excel file add sheet name or sheet number after
the filename, seperated by space.
--x-ax X_AX x_axis value column name
--y-ax Y_AX y_axis value column name
--reorder REORDER [REORDER ...]
user given reordering for any factor or column values
put name of the reorder column, followed by the new orders
seperated by spaces
Color parser: parse the color related arguments for boxplot:
--color COLOR, --border-color COLOR
color for outline or border of the boxes, [default is black]
--fill FILL, --box-color FILL
fill the inside of the boxes, [default is white]
--alpha ALPHA alpha or transparency value for the colors, [default is 1]
--palette PALETTE [PALETTE ...], --color-theme PALETTE [PALETTE ...]
color theme of the plot, [default is npg]
Grouping parser: parse the Facet/Group related arguments:
--facet FACET, --group FACET
facet by which column
--facet-col FACET_COL
How many columns for the faceting ; default is total number
of unique items in the facet columns
Label parser: parse the axis labels and title arguments:
--x-lab X_LAB label for x axis, [default is Cell line and Time after drug exposure]
--y-lab Y_LAB label for y axis, [default is Number of Foci per nucleus]
--title TITLE label for title of the plot, [default is gH2AX foci]
Dotplot parser: parse the dotplot related arguments to modify appearance:
--dot DOT Add 'jitter' or 'dotplot' to show dotplot
--dot-color DOT_COLOR
define outline color of the dotplot, [default is black]
--dot-fill DOT_FILL define fill color of the dotplot, [default is black]
--dot-alpha DOT_ALPHA
define color of the dotplot, [default is 0.2]
--dot-size DOT_SIZE define size of the dots in the plot, [default is 0.4]
--dot-val DOT_VAL, --dot-amount DOT_VAL
define amount of dots/jitter in the dotplot, [default is 0.06]
Save parser: parse the figure saving arguments:
--out OUT, --save-as OUT
directory and name for saving the plot, [default name boxplot.png]
--fig-size FIG_SIZE FIG_SIZE
Figure size width and height respectively, [default W/H are (20, 12)]
Statistics parser: parse the statistics related arguments:
--show-outliers Outliers will be shown
--stat statistics summary will be added when '--stat-comp' is declared
--stat-method STAT_METHOD
statistical method for testing, [default is t.test]
--stat-comp STAT_COMP [STAT_COMP ...]
list for statistical comparisons for testing
--stat-pos STAT_POS [STAT_POS ...]
y_axis position of the values for statistical comparisons
Axis parser: parse the axis modifying arguments:
--yscale YSCALE scale the y_axis by 'none', 'log2', 'log10', 'sqrt' [default is none]
--max-y MAX_Y maximum value to show in the y_axis, [default is 30]
--xtick-angle XTICK_ANGLE
rotate the tick values on the y_axis, [default is 90]
--legend LEGEND position the legend 'none', 'bottom', 'right', 'left' [default is top]
--hide-ticks All the ticks will be removed
Rscript --vanilla boxplotter_cli.R -hFollowing the command below and generate a basic boxplot
Rscript --vanilla boxplotter_cli.R --file mockData/MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --fill Time --save-as mockFigure/BasicBoxplot.png
# if the data is in the same directory/folder and you dont mention a filename for the generated image
# x-axis is Time and Color parameter is Cell
Rscript --vanilla boxplotter_cli.R --file MockFigure5C_3rdSheet.csv --x-ax Time --y-ax Foci --fill Cell
User can provide custom colors
Rscript --vanilla boxplotter_cli.R --file mockData/MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --fill Time --save-as mockFigure/CustomizeColorBoxplot.png --palette red green blue cyan gold gray pink navy
The color theme can be changed. For more themes visit this link
Rscript --vanilla boxplotter_cli.R --file mockData/MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --fill Time --palette jco --save-as mockFigure/JCOThemedBoxplot.png 
Rscript --vanilla boxplotter_cli.R --file mockData/MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --fill Cell --group Time --save-as mockFigure/GroupedBoxplot.png
size, amount and transparency of the dots can be specified
Rscript --vanilla boxplotter_cli.R --file mockData/MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --fill Cell --group Time --dot dotplot --dot-size 0.8 --dot-val 0.3 --dot-alpha 0.5 --save-as mockFigure/DotBoxplot.png
Color of dot can be specified
Rscript --vanilla boxplotter_cli.R --file mockData/MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --fill Cell --group Time --save-as mockFigure/DotBoxplot_gold.png --dot jitter --dot-color gold
Rscript --vanilla boxplotter_cli.R --file MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --fill Cell --group Time --dot jitter --dot-color gol --show-outliersTo add statistical summary of the dotplot i.e compare means via t-test can be performed
Rscript --vanilla boxplotter_cli.R --file mockData/MockFigure5C_3rdSheet.csv --x-ax Cell --y-ax Foci --facet Time --fill Cell --palette npg --dot dotplot --dot-size 0.6 --dot-val 0.6 --dot-alpha 0.2 --stat --stat-comp shGn1 shGn2 mu3-1 mu3-2 --save-as mockFigure/MockFigure5C_statistics.png
This module requires more works
Rscript --vanilla boxplotter_cli.R --file mockData/Mock_Figure5C.xlsx 3 --x-ax Cell --y-ax Foci --fill Cell --group Time --dot jitter --show-outliers --stat --stat-comp Glc4 PD-1 --dot-color gold --color steelblue --title "This is title of the plot" --save-as mockFigure/boxplotFromExcelSheet.png