diff --git a/README.md b/README.md index 40b317e..1010d96 100644 --- a/README.md +++ b/README.md @@ -106,6 +106,15 @@ logoplotwithcrosslink(pfm, C; rna=true) ``` which will automatically assume a uniform background of `[0.25, 0.25, 0.25, 0.25]`. +Use the command +``` +save_crosslinked_logoplot(pfm, background, C, "demo2.png") +``` +or +``` +save_crosslinked_logoplot(pfm, C, "demo2.png") # uniform background +``` +to save the plot. ### Multiplexed crosslinking tendencies @@ -126,6 +135,14 @@ You'd get Here, different colors indicate different crosslinking signatures, and their height is proportional to the crosslinking tendency at each position in the PWM. +Similar to above, use +``` +save_crosslinked_logoplot(pfm, background, C2, "demo3.png"; rna=true) +``` +to save the plot. + + + ## Plot your PWM with highlighted regions Sometimes you may have columns that you want to highlight, for example, when you have transcription factors binding sites embedded in a (long) transposable element (e.g. see figure 4 in this [paper](https://academic.oup.com/bioinformatics/article/39/6/btad378/7192989)). Then, what you can do is to provide a vector of `UnitRange{Int}` to highlight the regions of interest, e.g. ``` @@ -147,6 +164,9 @@ logoplot_with_highlight_crosslink(pfm, background, C2, highlighted_regions2) ![highlight-pfm](demo/demo5.png) +Use + + diff --git a/demo/demo2.png b/demo/demo2.png index 6fefe66..d57d268 100644 Binary files a/demo/demo2.png and b/demo/demo2.png differ diff --git a/demo/demo3.png b/demo/demo3.png index 03d7d4b..368cd65 100644 Binary files a/demo/demo3.png and b/demo/demo3.png differ