Yaamini’s Notebook: Remaining Analyses Part 19

Digital drawing board: Round 2

Steven commented on my previous post and said he liked the heatmap option! In my R script I played around with row clustering and color schemes. There are three decisions that need to be made:

  1. All data vs. differentially expressed subset
  2. Row clustering vs. no row clustering
  3. Color schemes

Decision 1: All data vs. differentially expressed subset

all-1

Figure 1. All data, now row clustering, standard color scheme

subset-1

Figure 2. Subset, no row clustering, standard color scheme

Decision 2: Row clustering vs. no row clustering

all-2

Figure 3. All data, row clustering, standard color scheme

subset-2

Figure 4. Subset, row clustering, standard color scheme

Decision 3: Color schemes

Blues

all-3

subset-3

Purples

all-4

subset-4

Purple-Blue

all-5

subset-5

Grey

all-6

subset-6

Purple-Green

all-7

subset-7

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Yaamini’s Notebook: Remaining Analyses Part 18

My better figure wasn’t actually good

I went back to the (digital) drawing board to make some more options.

Option 1: Dot charts

But this time, larger dots.

allpeptides

Figure 1. Average peptide abundance data across all sites.

diffexp

Figure 2. Differentially expressed average peptide abundance across all sites.

Option 2: Heatmaps

There aren’t large differences in the colors themselves (especially when looking at the figure with all peptide abundance data), so it’s not that exciting.

allheatmap

Figure 3. Average peptide abundance heatmap.

diffexpheatmap

Figure 4. Differentially expressed average peptide abundance across all sites.

Option 3: Bubble plot

I like Figure 6 more than Figure 5. If possible, I could scale all data by the smallest value to make the bubble sizes bigger and more dramatic.

xSiteyPeptide

Figure 5. Average normalized abundance across sites for each peptide. The points themselves are scaled such that larger points represent higher peptide abundance.

xSiteyAbundance

Figure 6. Average normalized abundance across sites. Points are scaled such that larger points represent higher peptide abundance, but all site data is grouped together. Points are color coded by peptide.

Option 4: Beeswarm plots

Suggestion from Steven! I think it’s a step up from the dot charts, but maybe not the best.

beeswarm

Figure 7. Beeswarm plot.

I wanted to make a volcano plot but it did not seem possible with my dataset. Perhaps I’m not searching for the right things in Google.

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