Difference between revisions of "Scripts"
From mn.ibv.aqua
(Created page with " Here you will find a collection of scripts and code snippets used in R, Python and other programming languages. == R scripts == == Python == Linear filming robot. This s...") |
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== R scripts == | == R scripts == | ||
| + | === Ecotoxicology === | ||
| + | |||
| + | ==== Comet assay ==== | ||
| + | Some helpful commands to read in all comet assay files simultaneously. Remember to convert the protected <code>.xls</code> files to <code>.csv</code> files, e.g. using LibreOffice<ref>https://www.libreoffice.org/</ref>. | ||
| + | * In R, navigate to the folder containing your <code>.csv</code> files using the <code>setwd()</code> command. | ||
| + | * Read in the tail intensity of the <code>.csv</code> files using the following command: <code>pre.data <- data.frame(sapply(list.files(pattern = "*.csv"), FUN = function(x) { read.csv(x, sep = ";", dec = ",")$Tail.Intensity }))</code>, but remember that you may have to adjust the separator and decimal characters. | ||
| + | * Calculate the median values of the 50 comets scored per sample: <code>pre.data <- sapply(pre.data, FUN = "median")</code>. | ||
| + | * Convert the data to a column-based data frame: <code>data <- data.frame(Tail.Intensity = stack(pre.data)[ , 1]</code>. | ||
| + | * Remember to add the necessary columns, describing e.g. concentration, locations, or treatments before further analysis. | ||
== Python == | == Python == | ||
Revision as of 08:33, 17 October 2016
Here you will find a collection of scripts and code snippets used in R, Python and other programming languages.
R scripts
Ecotoxicology
Comet assay
Some helpful commands to read in all comet assay files simultaneously. Remember to convert the protected .xls files to .csv files, e.g. using LibreOffice[1].
- In R, navigate to the folder containing your
.csvfiles using thesetwd()command. - Read in the tail intensity of the
.csvfiles using the following command:pre.data <- data.frame(sapply(list.files(pattern = "*.csv"), FUN = function(x) { read.csv(x, sep = ";", dec = ",")$Tail.Intensity })), but remember that you may have to adjust the separator and decimal characters. - Calculate the median values of the 50 comets scored per sample:
pre.data <- sapply(pre.data, FUN = "median"). - Convert the data to a column-based data frame:
data <- data.frame(Tail.Intensity = stack(pre.data)[ , 1]. - Remember to add the necessary columns, describing e.g. concentration, locations, or treatments before further analysis.
Python
Linear filming robot. This script allows to film up to 10 bottles. It will move from bottle to bottle and film each of the bottles for a specified number of seconds (HERE variable name).
