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davismcc / scaterPaperExtras

Discussion board for modifications to the scater paper
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Page 4: Figure 2 #13

Closed LTLA closed 8 years ago

LTLA commented 8 years ago

Six types of QC plot made easily available in the scater package.

A bit clunky, suggested:

Different types of QC plots that can be generated by scater.

Cumulative expression plot showing the proportion of the library accounted for by the x most-expressed features (from 1 to 500).

Or, just change it to:

Cumulative expression plot showing the proportion of the library accounted for by the top 1-500 most highly-expressed features.

Plot of the 50 most-expressed features (here, computed according to the highest total read counts) across all cells in the data set.

Don't really need the "here":

Plot of the 50 most highly-expressed features (computed according to the highest total read counts) across all cells in the data set.

The bars for each cell...

Surely we're talking about the bars for each gene, where each bar represents a cell. Suggested:

The bars for each gene...

Plot of frequency of expression (% of cells in which the feature is deemed expressed)...

Say what the "%" is in the caption:

Plot of frequency of expression (percentage of cells in which the feature is deemed expressed)...

I cat't read any of the gene names in 2C, nor the legends in 2E on a print-out. Maybe move 2F to supps (doesn't really add much here that's different from 2E), and reorganize to have A + B + D on the top row and C + E on the bottom, with expanded font sizes so we can actually see things. Possibly also chop off the ENSEMBL gunk from the gene names.

davismcc commented 8 years ago

Applied all these changes and Fig 2 looks much better! I've also implemented a feature_names_to_plot arg for plotHighestExprs so that you can use a column of fData for the feature names to use in the plot instead of being forced to use the featureNames of the SCESet.