274 lines
8.2 KiB
R
274 lines
8.2 KiB
R
mLigP
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mmLigP
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posC_lig
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ppi2P
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posC_ppi2
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peP
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theme_georgia <- function(...) {
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theme_gray(base_family = "sans", ...) +
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theme(plot.title = element_text(face = "bold"))
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}
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title_theme <- calc_element("plot.title", theme_georgia())
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###############################################################
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common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)
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# extract common legend
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common_legend_outcome = get_legend(mLigP +
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guides(color = guide_legend(nrow = 1)) +
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theme(legend.position = "top"))
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# ###############################################################
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# #================================
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# # Lig Affinity: outcome + site
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# #================================
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# ligT = paste0(common_bp_title, " ligand")
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# lig_affT = ggdraw() +
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# draw_label(
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# ligT,
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# fontfamily = title_theme$family,
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# fontface = title_theme$face,
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# #size = title_theme$size
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# size = 8
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# )
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# #-------------
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# # Outplot
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# #-------------
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# ligaffP = paste0(outdir_images
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# ,tolower(gene)
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# ,"_lig_oc.png")
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#
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# #svg(affP, width = 20, height = 5.5)
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# print(paste0("plot filename:", ligaffP))
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# png(ligaffP, units = "in", width = 6, height = 4, res = 300 )
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# cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome,
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# nrow = 2,
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# rel_heights = c(1,1)
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# ),
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# cowplot::plot_grid(mLigP, mmLigP, posC_lig
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# , nrow = 1
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# #, labels = c("A", "B", "C","D")
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# , rel_widths = c(1,1,1.8)
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# , align = "h"),
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# nrow = 2,
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# labels = c("A", ""),
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# label_size = 12,
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# rel_heights = c(1,8))
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# dev.off()
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# #############################################################
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# #================================
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# # PPI2 Affinity: outcome + site
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# #================================
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# ppi2T = paste0(common_bp_title, " PP-interface")
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# ppi2_affT = ggdraw() +
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# draw_label(
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# ppi2T,
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# fontfamily = title_theme$family,
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# fontface = title_theme$face,
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# #size = title_theme$size
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# size = 8
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# )
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#
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#
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# #-------------
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# # Outplot: PPI2
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# #-------------
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# ppiaffP = paste0(outdir_images
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# ,tolower(gene)
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# ,"_ppi2_oc.png")
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#
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# #svg(affP, width = 20, height = 5.5)
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# print(paste0("plot filename:", ppiaffP))
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# png(ppiaffP, units = "in", width = 6, height = 4, res = 300 )
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#
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#
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# cowplot::plot_grid(cowplot::plot_grid(ppi2_affT, common_legend_outcome,
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# nrow = 2,
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# rel_heights = c(1,1)),
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# cowplot::plot_grid(ppi2P, posC_ppi2
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# , nrow = 1
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# , rel_widths = c(1.2,1.8)
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# , align = "h"
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# , label_size = my_label_size),
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# nrow = 2,
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# labels = c("B", ""),
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# label_size = 12,
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# rel_heights = c(1,8)
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# )
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#
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# dev.off()
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# #############################################################
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#peP # pe counts
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#================================
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# PE + All position count
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#================================
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# peT_allT = ggdraw() +
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# draw_label(
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# paste0("All mutation sites"),
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# fontfamily = title_theme$family,
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# fontface = title_theme$face,
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# #size = title_theme$size
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# size = 8
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# )
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# #------------------------
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# # Outplot: lig+ppi2+pe
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# #------------------------
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# pe_allCL = paste0(outdir_images
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# ,tolower(gene)
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# ,"_pe_oc.png")
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#
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# #svg(affP, width = 20, height = 5.5)
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# print(paste0("plot filename:", pe_allCL))
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# png(pe_allCL, units = "in", width = 6, height = 4, res = 300 )
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#
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#
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# cowplot::plot_grid(peT_allT,
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# cowplot::plot_grid(peP, posC_all
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# , nrow = 1
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# , rel_widths = c(1, 2)
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# , align = "h"),
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# nrow = 2,
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# labels = c("C", "", ""),
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# label_size = 12,
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# rel_heights = c(1,8))
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#
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# dev.off()
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#===========================================
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# COMBINE ALL three
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#==========================================
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ligT = paste0(common_bp_title, " ligand")
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lig_affT = ggdraw() +
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draw_label(
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ligT,
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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#size = title_theme$size
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size = 8
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)
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p1 = cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome, nrow=2),
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cowplot::plot_grid(mLigP, mmLigP, posC_lig
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, nrow = 1
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, rel_widths = c(1,1,1.8)
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, align = "h"),
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nrow = 2,
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rel_heights = c(1,8)
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)
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#p1
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###########################################################
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ppi2T = paste0(common_bp_title, " PP-interface")
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ppi2_affT = ggdraw() +
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draw_label(
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ppi2T,
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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#size = title_theme$size
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size = 8
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)
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###########################################################
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p2 = cowplot::plot_grid(cowplot::plot_grid(ppi2_affT, common_legend_outcome, nrow=2),
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cowplot::plot_grid(ppi2P, posC_ppi2
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, nrow = 1
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, rel_widths = c(1.2,1.8)
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, align = "h"),
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nrow = 2,
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rel_heights = c(1,8)
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)
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#p2
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###########################################################
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# PE + All position count
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peT_allT = ggdraw() +
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draw_label(
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paste0("All mutation sites"),
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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#size = title_theme$size
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size = 8
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)
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p3 = cowplot::plot_grid(cowplot::plot_grid(peT_allT, nrow = 2
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, rel_widths = c(1,3),axis = "lr"),
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cowplot::plot_grid(
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peP2, posC_all,
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nrow = 2,
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rel_widths = c(1,1),
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align = "v",
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axis = "lr",
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rel_heights = c(1,8)
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),
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rel_heights = c(1,18),
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nrow = 2,axis = "lr")
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p3
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#===============
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# Final combine
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#===============
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w = 11.79
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h = 3.5
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mut_impact_CLP = paste0(outdir_images
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,tolower(gene)
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,"_mut_impactCLP.png")
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#svg(affP, width = 20, height = 5.5)
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print(paste0("plot filename:", mut_impact_CLP))
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png(mut_impact_CLP, units = "in", width = w, height = h, res = 300 )
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cowplot::plot_grid(p1, p2, p3
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, nrow = 1
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, labels = "AUTO"
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, label_size = 12
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, rel_widths = c(3,2,2)
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#, rel_heights = c(1)
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)
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dev.off()
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##################################################
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sensP
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consurfP
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#=================
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# Combine sensitivity + ConSurf
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# or ConSurf
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#=================
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w = 3
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h = 3
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# sens_conP = paste0(outdir_images
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# ,tolower(gene)
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# ,"_sens_cons_CLP.png")
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#
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# print(paste0("plot filename:", sens_conP))
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# png(sens_conP, units = "in", width = w, height = h, res = 300 )
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#
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# cowplot::plot_grid(sensP, consurfP,
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# nrow = 2,
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# rel_heights = c(1, 1.5)
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# )
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#
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# dev.off()
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conCLP = paste0(outdir_images
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,tolower(gene)
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,"_consurf_BP.png")
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print(paste0("plot filename:", conCLP))
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png(conCLP, units = "in", width = w, height = h, res = 300 )
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consurfP
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dev.off()
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#================================
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# Sensitivity numbers: geom_tile
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#================================
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sensCLP = paste0(outdir_images
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,tolower(gene)
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,"_sensN_tile.png")
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print(paste0("plot filename:", sensCLP))
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png(sensCLP, units = "in", width = 1, height = 1, res = 300 )
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sensP
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dev.off()
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