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Tanushree Tunstall 2022-08-27 23:11:44 +01:00
parent c3067b9176
commit da8a1069a8
3 changed files with 2 additions and 221 deletions
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4
scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
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@ -5,7 +5,7 @@
#=======
# output
#=======
outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
#outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
#cat("plots will output to:", outdir_images)
custom_cor <- function(data, mapping, method, ...){
@ -80,7 +80,7 @@ corr_plotdf = corr_data_extract(merged_df3
aff_dist_cols = colnames(corr_plotdf)[grep("Dist", colnames(corr_plotdf))]
static_cols = c("Log10(MAF)"
, "Log10(OR)"
#, "Log10(OR)"
)
############################################################
#=============================================

165
scripts/plotting/plotting_thesis/linage_bp_dist.R
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@ -1,165 +0,0 @@
#!/usr/bin/env Rscript
#########################################################
# TASK: Lineage plots [merged_df2]
# Count
# Diversity
# Average stability dist
# Avergae affinity dist: optional
#########################################################
#=======
# output
#=======
# outdir_images = paste0("~/git/Writing/thesis/images/results/"
# , tolower(gene), "/")
# cat("plots will output to:", outdir_images)
#########################################################
#===============
#Quick numbers checks
#===============
nsample_lin = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]
if ( all(table(nsample_lin$sensitivity)== table(nsample_lin$mutation_info_labels)) ){
cat("\nTotal no. of samples belonging to L1-l4 for", gene,":", nrow(nsample_lin)
, "\nCounting R and S samples")
if( sum(table(nsample_lin$sensitivity)) == nrow(nsample_lin) ){
cat("\nPASSNumbers cross checked:")
print(table(nsample_lin$sensitivity))
}
}else{
stop("Abort: Numbers mismatch. Please check")
}
########################################################################
###################################################
# Lineage barplots #
###################################################
my_xats = 8 # x axis text size # were 25
my_yats = 8# y axis text sized_lab_size
my_xals = 8 # x axis label size
my_yals = 8 # y axis label size
my_lls = 8 # legend label size
d_lab_size = 2.3
#===============================
# lineage sample and SNP count
#===============================
lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
, all_lineages = F
, x_categ = "sel_lineages"
, y_count = "p_count"
, use_lineages = c("L1", "L2", "L3", "L4")
, bar_fill_categ = "count_categ"
, display_label_col = "p_count"
, bar_stat_stype = "identity"
, d_lab_size = d_lab_size
, d_lab_col = "black"
, my_xats = my_xats # x axis text size
, my_yats = my_yats # y axis text sized_lab_size
, my_xals = my_xals # x axis label size
, my_yals = my_yals # y axis label size
, my_lls = my_lls # legend label size
, bar_col_labels = c("nsSNPs", "Total Samples")
, bar_col_values = c("grey50", "gray75")
, bar_leg_name = ""
, leg_location = "top"
, y_log10 = F
, y_scale_percent = FALSE
, y_label = c("Count")
)
lin_countP
#===============================
# lineage SNP diversity count
#===============================
lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
, x_categ = "sel_lineages"
, y_count = "snp_diversity"
#, all_lineages = F
, use_lineages = c("L1", "L2", "L3", "L4")
, display_label_col = "snp_diversity_f"
, bar_stat_stype = "identity"
, x_lab_angle = 90
, d_lab_size = d_lab_size
, my_xats = my_xats # x axis text size
, my_yats = my_yats # y axis text sized_lab_size
, my_xals = my_xals # x axis label size
, my_yals = my_yals # y axis label size
, my_lls = my_lls # legend label size
, y_log10 = F
, y_scale_percent = F
, leg_location = "top"
, y_label = "Percent" #"SNP diversity"
, bp_plot_title = "nsSNP diversity"
, title_colour = "black" #"chocolate4"
, subtitle_text = NULL
, sts = 10
, subtitle_colour = "#350E20FF")
lin_diversityP
###################################################
# Stability dist #
###################################################
# scaled_cols_stability = c("duet_scaled"
# , "deepddg_scaled"
# , "ddg_dynamut2_scaled"
# , "foldx_scaled"
# , "avg_stability_scaled")
my_ats = 8 # x axis text size # were 25
my_als = 8# y axis text sized_lab_size
my_leg_ts = 8 # x axis label size
my_leg_title = 8 # y axis label size
my_strip_ts = 8 #
my_xlabel = paste0("Average stability ", "(", stability_suffix, ")"); my_xlabel
#plotdf = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]
linP_dm_om = lineage_distP(merged_df2
, with_facet = F
, x_axis = "avg_stability_scaled"
, y_axis = "lineage_labels"
, x_lab = my_xlabel
, use_lineages = c("L1", "L2", "L3", "L4")
#, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
, fill_categ = "sensitivity"
, fill_categ_cols = c("red", "blue")
, label_categories = c("Resistant", "Sensitive")
, leg_label = "Mutation group"
, my_ats = my_ats # axis text size
, my_als = my_als # axis label size
, my_leg_ts = my_leg_ts
, my_leg_title = my_leg_title
, my_strip_ts = my_strip_ts
, alpha = 0.56
)
linP_dm_om
###################################################
# Affinity dist [OPTIONAL] #
###################################################
# scaled_cols_affinity = c("affinity_scaled"
# , "mmcsm_lig_scaled"
# , "mcsm_ppi2_scaled"
# , "mcsm_na_scaled"
# , "avg_lig_affinity_scaled")
# lineage_distP(merged_df2
# , with_facet = F
# , x_axis = "avg_lig_affinity_scaled"
# , y_axis = "lineage_labels"
# , x_lab = my_xlabel
# , use_lineages = c("L1", "L2", "L3", "L4")
# #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
# , fill_categ = "sensitivity"
# , fill_categ_cols = c("red", "blue")
# , label_categories = c("Resistant", "Sensitive")
# , leg_label = "Mutation group"
# , my_ats = 22 # axis text size
# , my_als = 22 # axis label size
# , my_leg_ts = 22
# , my_leg_title = 22
# , my_strip_ts = 22
# , alpha = 0.56
# )

54
scripts/plotting/plotting_thesis/linage_bp_dist_layout.R
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@ -1,54 +0,0 @@
#!/usr/bin/env Rscript
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist.R")
###########################################
# TASK: generate plots for lineage
# Individual plots in
#lineage_bp_both.R
#linage_dist_ens_stability.R
###########################################
# svg
# linPlots_combined = paste0(outdir_images
# , tolower(gene)
# ,"_linP_combined.svg")
#
# cat("\nOutput plot:", linPlots_combined)
# svg(linPlots_combined, width = 18, height = 12)
#
# cowplot::plot_grid(
# cowplot::plot_grid(lin_countP, lin_diversityP
# , nrow = 2
# , rel_heights = c(1.2,1)
# , labels = "AUTO"
# , label_size = my_label_size),
# NULL,
# linP_dm_om,
# nrow = 1,
# labels = c("", "", "C"),
# label_size = my_label_size,
# rel_widths = c(35, 3, 52)
# )
# dev.off()
# png
my_label_size = 12
linPlots_combined = paste0(outdir_images
, tolower(gene)
,"_linP_combined.png")
cat("\nOutput plot:", linPlots_combined)
png(linPlots_combined, width = 9, height = 6, units = "in" ,res = 300)
cowplot::plot_grid(
cowplot::plot_grid(lin_countP, lin_diversityP
, nrow = 2
, rel_heights = c(1.2,1)
, labels = "AUTO"
, label_size = my_label_size),
NULL,
linP_dm_om,
nrow = 1,
labels = c("", "", "C"),
label_size = my_label_size,
rel_widths = c(35, 3, 52)
)
dev.off()