58 lines
1.8 KiB
R
58 lines
1.8 KiB
R
setwd("~/git/LSHTM_analysis/scripts/plotting/")
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source("Header_TT.R")
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source("../functions/lf_bp.R")
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# ================================================
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# Data: run get_plotting_data.R
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# to get the long format data to test this function
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# drug = "streptomycin"
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# gene = "gid"
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# source("get_plotting_dfs.R")
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# ==================================================
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######################
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# Make plot: ggplot
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######################
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lf_bp(lf_df = lf_encomddg
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, p_title = "ENCoM-DDG"
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, colour_categ = "ddg_encom_outcome"
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, x_grp = "mutation_info"
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, y_var = "param_value"
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, facet_var = "param_type"
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, n_facet_row = 1
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, y_scales = "free_y"
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, colour_bp_strip = "khaki2"
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, dot_size = 3
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, dot_transparency = 0.3
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, violin_quantiles = c(0.25, 0.5, 0.75)
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, my_ats = 22 # axis text size
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, my_als = 20 # axis label size
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, my_fls = 20 # facet label size
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, my_pts = 22 # plot title size
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, make_boxplot = F
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, bp_width = "auto"
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, add_stats = T
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, stat_grp_comp = c("DM", "OM")
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, stat_method = "wilcox.test"
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, my_paired = FALSE
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, stat_label = c("p.format", "p.signif") )
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#wilcox.test(wf_encomdds$`EnCOM ΔΔS`[wf_encomdds$mutation_info == "DM"]
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# , wf_encomdds$`EnCOM ΔΔS`[wf_encomdds$mutation_info == "OM"])
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######################
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# Make plot: plotly
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######################
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# FIXME: This labels are not working as I want!
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# lf_bp_plotly(lf_df = lf_deepddg
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# , p_title = "DeepDDG"
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# , colour_categ = "deepddg_outcome"
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# , x_grp = "mutation_info"
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# , y_var = "param_value"
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# , facet_var = "param_type"
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# , n_facet_row = 1
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# , y_scales = "free_y"
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# , colour_bp_strip = "khaki2"
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# , dot_size = 3
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# , dot_transparency = 0.3
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# , violin_quantiles = c(0.25, 0.5, 0.75)
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# )
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