Are you bored to do the FACS data statistic post flowjo handling?
USE FACSHAND!
Facshand script is based on R for statistic and plot of FACS data exported from Flowjo. You can easily caculate and plot your FACS data by typing the following code in your terminal.
Rscript path/facshand.R path_dir/
or run the script on R console as the following codes:
path <- "path_dir"
source("path/facshand.R", chdir = TRUE)
You can directly drag your script file and directory to the console to acheive the paths.
Make sure that R has been installed in your OS with ggplot2 and Hmisc packages installed.
install.packages("ggplot2")
install.packages("Hmisc")
install.packages("acepack")
The input files are as follows, keep these files in your path_dir directory.
-
rawdata.csv
transform xlsx file derived from flowjo to csv;
-
celltype.csv
with the header of "celltype", input the exact names of the subsets to be calculated;
-
group.csv
with the header of "group", input the exact names of your groups;
-
cellnumber.csv
with two colunms of "tissue" and "number", tissue refers to the exact name of your FACS sample names, and number refers to the cell number (x 104) for caculation; notice that the sample name should be prefixed with group name, eg WT_whatever, ko-dmso-whatever.
* make sure that your subset names are not duplicated, even partially duplicated names are not allowed, ignore cases.
The output files include
-
data.csv
contains the population and cell number caculated data;
-
statistic.txt
refers to the statistics for the compared groups using students' t test between two groups. If multi groups are inputted, one-way anova is used for statistic;
-
plots
named by your celltype names in tiff format, including population and cell number caculated dot plots with p-values. The plots may not meet the submission demands, but are enough for the presentation in lab meeting (maybe) :p .
20200923_update: modify to make x axis display as the same sequence as group.csv shown, modify to tolerate the most frequently used symbol in FACS gating "+".
20200812_update: support the rawdata files exported from flowjo version <= 10.1, support direct run on R console, add notices.