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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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15
scripts/functions/bp_lineage.R
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@ -13,15 +13,15 @@ lin_count_bp <- function( lf_data = lin_lf
, display_label_col = "p_count"
, bar_stat_stype = "identity"
, x_lab_angle = 90
, d_lab_size = 5
, d_lab_size = 2.3
, d_lab_hjust = 0.5
, d_lab_vjust = 0.5
, d_lab_col = "black"
, my_xats = 20 # x axis text size
, my_yats = 20 # y axis text size
, my_xals = 22 # x axis label size
, my_yals = 22 # y axis label size
, my_lls = 22 # legend label size
, my_xats = 8 # x axis text size
, my_yats = 8 # y axis text size
, my_xals = 10 # x axis label size
, my_yals = 10 # y axis label size
, my_lls = 10 # legend label size
, bar_col_labels = c("Mutations", "Total Samples")
, bar_col_values = c("grey50", "gray75")
, bar_leg_name = ""
@ -56,7 +56,8 @@ lin_count_bp <- function( lf_data = lin_lf
, axis.title.y = element_text(size = my_yals
, colour = "black")
, legend.position = leg_location
, legend.text = element_text(size = my_lls)) +
, legend.text = element_text(size = my_lls)
, legend.key.size = unit(my_lls, 'pt')) +
geom_label(aes(label = eval(parse(text = display_label_col)))
, size = d_lab_size

13
scripts/functions/bp_lineage_diversity.R
View file

@ -14,15 +14,15 @@ lin_count_bp_diversity <- function( lf_data = lin_wf
, display_label_col = "snp_diversity_f"
, bar_stat_stype = "identity"
, x_lab_angle = 90
, d_lab_size = 5
, d_lab_size = 2.3
, d_lab_hjust = 0.5
, d_lab_vjust = 0.5
, d_lab_col = "black"
, my_xats = 20 # x axis text size
, my_yats = 20 # y axis text size
, my_xals = 22 # x axis label size
, my_yals = 22 # y axis label size
, my_lls = 22 # legend label size
, my_xats = 8 # x axis text size
, my_yats = 8 # y axis text size
, my_xals = 10 # x axis label size
, my_yals = 10 # y axis label size
, my_lls = 10 # legend label size
, bar_col_labels = "" #c("Mutations", "Total Samples")
, bar_col_values = c("gray50", "gray75")
, bar_leg_name = ""
@ -64,6 +64,7 @@ lin_count_bp_diversity <- function( lf_data = lin_wf
, colour = "black")
, legend.position = leg_location
, legend.text = element_text(size = my_lls)
, legend.key.size = unit(my_lls, 'pt')
, plot.title = element_text(size = my_lls
, colour = title_colour
, hjust = 0.5)

18
scripts/functions/corr_plot_data.R
View file

@ -7,9 +7,6 @@
# LigDist_colname #from globals: plotting_globals.R
# ppi2Dist_colname #from globals: plotting_globals.R
# naDist_colname #from globals: plotting_globals.R
geneL_normal = c("pnca")
geneL_na = c("gid", "rpob")
geneL_ppi2 = c("alr", "embb", "katg", "rpob")
corr_data_extract <- function(df
, gene
@ -75,11 +72,24 @@ corr_data_extract <- function(df
if (tolower(gene)%in%geneL_na){
colnames_to_extract = c(common_colnames,"mcsm_na_affinity", naDist_colname)
display_colnames = c(display_common_colnames, "mCSM-NA", "NCA-Dist")
display_colnames = c(display_common_colnames, "mCSM-NA", "NA-Dist")
corr_df = df[,colnames_to_extract]
colnames(corr_df) = display_colnames
}
# SPECIAL case for rpob as it exists in both ppi and na
if (tolower(gene)%in%c("rpob")){
colnames_to_extract = c(common_colnames
, "mcsm_ppi2_affinity", ppi2Dist_colname
, "mcsm_na_affinity", naDist_colname)
display_colnames = c(display_common_colnames
,"mCSM-PPI2", "PPI-Dist"
,"mCSM-NA", "NA-Dist" )
corr_df = df[,colnames_to_extract]
colnames(corr_df) = display_colnames
}
# [optional] arg: extract_scaled_cols
if (extract_scaled_cols){
cat("\nExtracting scaled columns as well...\n")

6
scripts/functions/dm_om_data.R
View file

@ -734,7 +734,7 @@ dm_om_wf_lf_data <- function(df
# mcsm-ppi2 affinity
# data filtered by cut off
#========================
if (tolower(gene)%in%geneL_ppi2){
if (tolower(gene)%in%geneL_ppi2 || tolower(gene)%in%geneL_both){
#-----------------
# mCSM-PPI2: WF and lF
#-----------------
@ -776,13 +776,11 @@ dm_om_wf_lf_data <- function(df
}
#====================
# mcsm-NA affinity
# data filtered by cut off
#====================
if (tolower(gene)%in%geneL_na){
if (tolower(gene)%in%geneL_na|| tolower(gene)%in%geneL_both){
#---------------
# mCSM-NA: WF and lF
#-----------------

11
scripts/functions/lineage_dist.R
View file

@ -20,11 +20,11 @@ lineage_distP <- function(plotdf
, fill_categ = "mutation_info_labels"
, fill_categ_cols = c("#E69F00", "#999999")
, label_categories = c("LABEL1", "LABEL2")
, my_ats = 15 # axis text size
, my_als = 20 # axis label size
, my_leg_ts = 16
, my_leg_title = 16
, my_strip_ts = 20
, my_ats = 15 # 15 axis text size
, my_als = 20 # 20 axis label size
, my_leg_ts = 16 #16
, my_leg_title = 16 #16
, my_strip_ts = 20 #20
, leg_pos = c(0.8, 0.9)
, leg_pos_wf = c("top", "left", "bottom", "right")
, leg_dir_wf = c("horizontal", "vertical")
@ -57,6 +57,7 @@ lineage_distP <- function(plotdf
, axis.title.y = element_blank()
, strip.text = element_text(size = my_strip_ts)
, legend.text = element_text(size = my_leg_ts)
, legend.key.size = unit(my_leg_ts, 'pt')
, legend.title = element_text(size = my_leg_title)
, legend.position = c(0.8, 0.9)) +
labs(x = x_lab

3
scripts/functions/position_count_bp.R
View file

@ -132,7 +132,8 @@ site_snp_count_bp <- function (plotdf
scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
geom_label(stat = "count", aes(label = ..count..)
, color = "black"
, size = geom_ls) +
, size = geom_ls
, position = position_dodge2(width = 1)) +
theme(axis.text.x = element_text(size = axis_text_size
, angle = 0)
, axis.text.y = element_text(size = axis_text_size