56 lines
1.9 KiB
R
56 lines
1.9 KiB
R
# Tweak for layout, fonts, and text sizes.
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#svg('~/tmp/foo.svg', width=10, height=10, )
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# Set the width/height to inches for print. 300 dpi is reasonably ok for "draft"
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# output. To raise quality while preserving sanity, increase 'res' and
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# DO NOT alter font/point/line sizes
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#- [X] Black text for "Corr:" or replace with Rho symbol
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#- [X] 0/1 == R/S
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#- [X] "rho" symbol instead of "Corr:" text
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#- [X] Dot size a bit smaller
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#- [X] Plot lines slightly thinner
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#
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#
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png('~/tmp/foo.png',
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width=10,
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height=10,
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units="in",
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res=300)
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#
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#corr_plotting_df = corr_df_ps
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colnames(corr_plotdf)
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corr_plotting_df = subset(corr_plotdf, select = -c(ethambutol,`Log10(OR)`,`-Log10(P)`, ASA, RSA, KD, RD
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, FoldX
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, DeepDDG
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, Dynamut2 ))
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colnames(corr_plotting_df)
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#ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)-1),
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ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)),
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upper = list(continuous = wrap('cor',
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method = "spearman",
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use = "pairwise.complete.obs",
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title="ρ",
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digits=2,
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title_args=c(colour="black")
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)
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),
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lower = list(
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continuous = wrap("points", alpha = 0.7, size=0.5),
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combo = wrap("dot", alpha = 0.7, size=0.5)
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),
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aes(colour = factor(ifelse(dst_mode==0, "S", "R")), alpha = 0.5),
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title="Stability") +
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scale_colour_manual(values = c("red", "blue")) +
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scale_fill_manual(values = c("red", "blue")) +
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theme(
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text = element_text(size=12, face="bold")
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)
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dev.off()
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#Check all plots with LSHTM_analysis/scripts/plotting/plotting_colnames.R
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