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/6-Figure scripts/Fig E3.r
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| a | b/6-Figure scripts/Fig E3.r | ||
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| 1 | library(readxl) |
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| 2 | library(ggplot2) |
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| 3 | library(ggrepel) |
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| 4 | |||
| 5 | excel_sheets("Fig E3 Source Data.xlsx") |
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| 6 | |||
| 7 | # Figure E3a ------------------ |
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| 8 | dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Metabolome") |
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| 9 | |||
| 10 | FigE3a.metab <- ggplot(dat) + |
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| 11 | geom_point(aes(x=NEU, y=EOS), size=2)+ |
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| 12 | theme_bw()+ theme(panel.grid = element_blank()) + |
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| 13 | geom_hline(yintercept = 0, linetype="twodash") + |
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| 14 | geom_hline(yintercept = 1, linetype="dashed") + |
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| 15 | geom_hline(yintercept = -1, linetype="dashed") + |
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| 16 | geom_vline(xintercept = -1, linetype="dashed") + |
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| 17 | geom_vline(xintercept = 0, linetype="twodash") + |
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| 18 | geom_vline(xintercept = 1, linetype="dashed") + |
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| 19 | xlab("Correlation NEU: Directionality x - log(P)")+ |
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| 20 | ylab("Correlation EOS: Directionality x - log(P)")+ |
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| 21 | ggtitle("Differential MetaB modules") |
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| 22 | FigE3a.metab |
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| 23 | |||
| 24 | |||
| 25 | # Figure E3b ------------------ |
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| 26 | dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Transcriptome") |
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| 27 | |||
| 28 | FigE3b.hostT <- ggplot(dat) + |
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| 29 | geom_point(aes(x=NEU, y=EOS), size=2)+ |
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| 30 | theme_bw()+ theme(panel.grid = element_blank()) + |
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| 31 | geom_hline(yintercept = 0, linetype="twodash") + |
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| 32 | geom_hline(yintercept = 1, linetype="dashed") + |
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| 33 | geom_hline(yintercept = -1, linetype="dashed") + |
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| 34 | geom_vline(xintercept = -1, linetype="dashed") + |
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| 35 | geom_vline(xintercept = 0, linetype="twodash") + |
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| 36 | geom_vline(xintercept = 1, linetype="dashed") + |
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| 37 | xlab("Correlation NEU: Directionality x - log(P)")+ |
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| 38 | ylab("Correlation EOS: Directionality x - log(P)")+ |
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| 39 | ggtitle("Differential HostT modules") |
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| 40 | FigE3b.hostT |
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| 41 | |||
| 42 | |||
| 43 | # Figure E3c ------------------ |
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| 44 | dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Sputum Proteome") |
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| 45 | colnames(dat)[1] <- "Label" |
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| 46 | |||
| 47 | FigE3c.sputum <- ggplot(dat) + |
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| 48 | geom_point(aes(x=NEU, y=EOS), size=2)+ |
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| 49 | geom_text_repel(aes(x=NEU,y=EOS, label = Label),size=3) + |
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| 50 | theme_bw()+ theme(panel.grid = element_blank()) + |
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| 51 | geom_hline(yintercept = 0, linetype="twodash") + |
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| 52 | geom_hline(yintercept = 1, linetype="dashed") + |
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| 53 | geom_hline(yintercept = -1, linetype="dashed") + |
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| 54 | geom_vline(xintercept = -1, linetype="dashed") + |
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| 55 | geom_vline(xintercept = 0, linetype="twodash") + |
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| 56 | geom_vline(xintercept = 1, linetype="dashed") + |
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| 57 | xlab("Correlation NEU: Directionality x - log(P)")+ |
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| 58 | ylab("Correlation EOS: Directionality x - log(P)")+ |
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| 59 | ggtitle("Differential sputum proteins") |
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| 60 | FigE3c.sputum |
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| 61 | |||
| 62 | |||
| 63 | # Figure E3d ------------------ |
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| 64 | dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Serum Proteome") |
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| 65 | colnames(dat)[1] <- "Label" |
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| 66 | |||
| 67 | FigE3d.serum <- ggplot(dat) + |
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| 68 | geom_point(aes(x=NEU2, y=EOS), size=2)+ |
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| 69 | geom_text_repel(aes(x=NEU2,y=EOS, label = Label),size=3) + |
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| 70 | theme_bw()+ theme(panel.grid = element_blank()) + |
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| 71 | # geom_hline(yintercept = 0, linetype="twodash") + |
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| 72 | geom_hline(yintercept = 1, linetype="dashed") + |
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| 73 | geom_hline(yintercept = -1, linetype="dashed") + |
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| 74 | geom_vline(xintercept = -1, linetype="dashed") + |
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| 75 | # geom_vline(xintercept = 0, linetype="twodash") + |
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| 76 | geom_vline(xintercept = 1, linetype="dashed") + |
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| 77 | xlab("Correlation NEU: Directionality x - log(P)")+ |
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| 78 | ylab("Correlation EOS: Directionality x - log(P)")+ |
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| 79 | ggtitle("Differential serum proteins") |
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| 80 | FigE3d.serum |
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| 81 | |||
| 82 | # integrate Figures |
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| 83 | library(ggpubr) |
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| 84 | |||
| 85 | FigE3 <- ggarrange(FigE3a.metab, FigE3b.hostT, FigE3c.sputum, FigE3d.serum) |
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| 86 |