In hirscheylab/tidybiology: Utility Functions and Data Sets for Tidy Biology

Create a style you like to use later for all the other plots

You need to load ggplot2 library before you define your style in a list.

Load data

Load scRNAseq data from our library below.

Preview data structure by the method you prefer

Generate plots

• For the questions below, feel free to use the ggplot2 builder as an assistance.
• Remember to label you axes and title your legends and plots properly.

Which gene type has a bigger transcript length?

Choose the range of transcript length that you think is reasonable to be used for the plot.

• The length might not make sense and thus can potentially be an artifact that you want to remove.
• You may need to adjust the plot width or turn the axis texts on x-axis with an angle to avoid overlapping.

Which organ (excluding the "other" category) has a higher average transcript length?

Excluding extreme outliers by strategically filtering the data can help you focus more. Also use ggsignif to label out the p values of 2 organs that you're interested in color red so people can easily observe whether the difference is significant.

For the gene type that is expressed in more organ types, in which organ does that gene type have the highest average GC content?

Please use the viridis coloring scheme here.

Pick 2 cells that you like to compare

Let's focus on the organ types other than "other". Do you think these 2 cells are more likely to be of the same cell type or different cell types?

Add marginal histograms around both axes by ggExtra. Adding a y=x line on the plot can help you approximate the correlation of these 2 cells' RNA.

• If same cell type, which organ(s) are they most likely coming from?
• If different cell types, which organ(s) does each of the 2 cells might come from?

Explore ggplot 2 extensions

Discover a new ggplot2 extension from https://exts.ggplot2.tidyverse.org/gallery/ and try to use it below in a plot that you already made previously.

Suggestion: use gghalves extension to change the right half of geom_boxplots into half violin plots for information about distribution.

hirscheylab/tidybiology documentation built on May 20, 2022, 10:55 p.m.