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lots of per-plot configs

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This commit is contained in:
Tanushree Tunstall 2022-08-22 21:56:13 +01:00
parent 13999a477d
commit 04253b961f
36 changed files with 5121 additions and 540 deletions
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48
scripts/plotting/plotting_thesis/dm_om_plots.R
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@ -36,11 +36,11 @@ genomicsP = lf_bp2(genomics_dataP
genomicsP
#check
wilcox.test(wf_dist_genP$`Log10(MAF)`[wf_dist_genP$mutation_info_labels=="R"]
, wf_dist_genP$`Log10(MAF)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)
tapply(wf_dist_genP$`Log10(MAF)`, wf_dist_genP$mutation_info_labels, summary)
# #check
# wilcox.test(wf_dist_genP$`Log10(MAF)`[wf_dist_genP$mutation_info_labels=="R"]
# , wf_dist_genP$`Log10(MAF)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)
#
# tapply(wf_dist_genP$`Log10(MAF)`, wf_dist_genP$mutation_info_labels, summary)
#-------------------
# Distance data plot:
@ -61,16 +61,16 @@ distanceP = lf_bp2(dist_dataP
distanceP
# check
wilcox.test(wf_dist_genP$`PPI Dist(Å)`[wf_dist_genP$mutation_info_labels=="R"]
, wf_dist_genP$`PPI Dist(Å)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)
wilcox.test(wf_dist_genP$`Lig Dist(Å)`[wf_dist_genP$mutation_info_labels=="R"]
, wf_dist_genP$`Lig Dist(Å)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)
tapply(wf_dist_genP$`PPI Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)
tapply(wf_dist_genP$`Lig Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)
# # check
# wilcox.test(wf_dist_genP$`PPI Dist(Å)`[wf_dist_genP$mutation_info_labels=="R"]
# , wf_dist_genP$`PPI Dist(Å)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)
#
# wilcox.test(wf_dist_genP$`Lig Dist(Å)`[wf_dist_genP$mutation_info_labels=="R"]
# , wf_dist_genP$`Lig Dist(Å)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)
#
# tapply(wf_dist_genP$`PPI Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)
#
# tapply(wf_dist_genP$`Lig Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)
#-------------------
@ -100,7 +100,9 @@ if (tolower(gene)%in%geneL_ppi2){
levels(dist_data_ppi2$param_type)
distanceP_ppi2 = lf_bp2(dist_data_ppi2
#, p_title = ""
, violin_quantiles = c(0.5), monochrome = F)
, violin_quantiles = c(0.5)
, dot_transparency = 0.2
, monochrome = F)
distanceP_ppi2
}
@ -109,9 +111,9 @@ if (tolower(gene)%in%geneL_na){
#-------------------
# Distance data plot: NADist
#--------------------
levels(dist_dataP$param_type)[[3]]
levels(dist_dataP$param_type)[[2]]
#Lig Dist(Å), PPI Dist(Å)
dist_data_na = dist_dataP[dist_dataP$param_type%in%c(levels(dist_dataP$param_type)[[3]]),]
dist_data_na = dist_dataP[dist_dataP$param_type%in%c(levels(dist_dataP$param_type)[[2]]),]
dist_data_na$param_type = factor(dist_data_na$param_type)
table(dist_data_na$param_type)
levels(dist_data_na$param_type)
@ -233,9 +235,9 @@ table(lf_mcsm_ligP$param_type)
mcsmligP = lf_bp2(lf_mcsm_ligP
#, p_title = ""
, violin_quantiles = c(0.5), monochrome = F
, dot_transparency = 1)
, dot_transparency = 0.8)
mcsmligP
#=================
# Plot: mmCSM-lig2
#=================
@ -248,7 +250,7 @@ table(lf_mmcsm_lig2P$param_type)
mcsmlig2P = lf_bp2(lf_mmcsm_lig2P
#, p_title = ""
, violin_quantiles = c(0.5), monochrome = F
, dot_transparency = 1)
, dot_transparency = 0.8)
mcsmlig2P
@ -265,7 +267,7 @@ if (tolower(gene)%in%geneL_ppi2){
mcsmppi2P = lf_bp2(lf_mcsm_ppi2P
#, p_title = ""
, violin_quantiles = c(0.5), monochrome = F
, dot_transparency = 1)
, dot_transparency = 0.3)
}
@ -282,7 +284,7 @@ if (tolower(gene)%in%geneL_na){
mcsmnaP = lf_bp2(lf_mcsm_naP
#, p_title = ""
, violin_quantiles = c(0.5), monochrome = F
, dot_transparency = 1)
, dot_transparency = 0.4)
}