From 94ad2b9974f8e6b3d9bbdd5750e6acf6f7612040 Mon Sep 17 00:00:00 2001 From: Cosmin SAVEANU <cosmin.saveanu@pasteur.fr> Date: Mon, 3 Jun 2019 14:30:48 +0200 Subject: [PATCH] Update README.md, Categorical heatmaps/README.md files --- Categorical heatmaps/README.md | 18 ++++++++++++++++++ README.md | 4 +--- 2 files changed, 19 insertions(+), 3 deletions(-) create mode 100644 Categorical heatmaps/README.md diff --git a/Categorical heatmaps/README.md b/Categorical heatmaps/README.md new file mode 100644 index 0000000..c5ebf6b --- /dev/null +++ b/Categorical heatmaps/README.md @@ -0,0 +1,18 @@ +The script `generate_heatmap.R` can be used to represent a table of data in the form of an adjusted heat map. It uses two packages that need to be installed, `ggplot2` and `reshape2`. The input of the script is a tab delimited file text that looks like this: + + + +What the script does: + +1. Takes the maximum of each line (thus maximum value for each gene, in our example) and divides the values with that maximum. Thus, for each gene, we get values between 0 and 1 (per row). + +2. Transforms the obtained values to categories: for example, if a value is between 0.25 and 0.5, that value will belong to the "25%-50%" category + +3. Use `ggplot2` to generate a graphical representation of the categories in a table. If the plot is satisfactory, it can be saved, with the `ggsave` function. + +![alt output from ggplot2][output] + +[output]: ./heatplotexampleoutput.png + + +The final results can be further enhanced and modified in Inkscape or Adobe illustrator. \ No newline at end of file diff --git a/README.md b/README.md index 705f29b..0af675f 100644 --- a/README.md +++ b/README.md @@ -1,3 +1 @@ -First project on GitLab. - -Will most likely import form redmine. \ No newline at end of file +A repository of R snippets, mostly for creating graphical visualization of data. \ No newline at end of file -- GitLab