Figures needed for paper

[sr320]

• [x] Gene level differential expression (lack of) Volcano Plot @kubu4
• [x] Transcript level differential expression (lack of) Volcano Plot @kubu4
• [x] Correlation Matrices for Gene Variation @AHuffmyer
• [x] Maximum number of transcripts shift within sex @yaaminiv (table)
• [x] Predominant transcript shift within sex @yaaminiv (table)
• [x] Spurious transcription - more analysis need see: #90, #91
• [x] Correlation matrix gene methylation and expression
• [x] Maximum number of transcripts shift within sex - based on methylation @yaaminiv
• [x] Predominant transcript shift within sex - based on methylation @yaaminiv
• [x] Spurious transcription - more analysis need #90, #91 - based on methylation

[AHuffmyer]

Added supplementary figure to document for correlation matrices, left unnumbered for now.

[kubu4]

Gene level differential expression (lack of) Volcano Plot @kubu4 Transcript level differential expression (lack of) Volcano Plot @kubu4

Do we want volcano plots for all of the comparisons (e.g. male vs. female, controls vs. exposed, female controls vs. female exposed, etc) of gene and transcript expression?

[sr320]

@kubu4 no all analysis will be within sex - thus just need one plot per sex

[kubu4]

Volcano plots are here:

https://github.com/sr320/ceabigr/blob/main/output/18-differential-gene-expression-ballgown/figures/

Per lab meeting today:

• remove distinguishing color for genes/transcripts with p-value <= 0.05
• create multipanel figure

[yaaminiv]

Maximum number of transcripts shift within sex @yaaminiv (table) Predominant transcript shift within sex @yaaminiv (table)

Table added in the paper

[yaaminiv]

Predominant transcript shift within sex - based on methylation @yaaminiv

Supplemental figure added to paper: https://github.com/sr320/ceabigr/blob/main/output/42-predominant-isoform/pred-isoform-change-meth-distribution.pdf

Another supp figure option, but I opted for the one above since that visualizes change in methylation (which was in the model): https://github.com/sr320/ceabigr/blob/main/output/42-predominant-isoform/pred-isoform-meth-exp-xy.pdf

[yaaminiv]

Maximum number of transcripts shift within sex - based on methylation @yaaminiv

Supplemental figure to be added to paper/supp directory: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/max-trans-change-meth-distribution.pdf

Another supp figure option: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/max-trans-meth-exp-xy.pdf

[AHuffmyer]

Added figures for alternative splicing to document and supplementary materials. Links to code and figure in respective comments in manuscript. Notebook post about analysis here: https://ahuffmyer.github.io/ASH_Putnam_Lab_Notebook/Analysis-of-Variance-Simultaneous-Component-Analyses-ASCA-for-CEABIGR-project/

[yaaminiv]

@AHuffmyer color scheme for plots:

require(RColorBrewer)

plotColors <- RColorBrewer::brewer.pal(9, "Greens")

plotColors[5] for control and plotColors[8] for exposed. Thanks!

[yaaminiv]

Spurious transcription - more analysis need https://github.com/sr320/ceabigr/issues/90, https://github.com/sr320/ceabigr/issues/91 - based on methylation

Figure made and added to the main text

https://github.com/sr320/ceabigr/blob/main/output/78-asca-methdiff/methylation-patterns-splice-type.pdf