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added plots for thesis

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This commit is contained in:
Tanushree Tunstall 2022-08-03 21:32:47 +01:00
parent 41c4996426
commit aabe466599
17 changed files with 24 additions and 2913 deletions
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2
scripts/functions/lineage_plot_data.R
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@ -34,6 +34,8 @@ lineage_plot_data <- function(df
################################################################
# Get WF and LF data with lineage count, and snp diversity
################################################################
df[lineage_column_name] =
# Initialise output list
lineage_dataL = list(
lin_wf = data.frame()

5
scripts/functions/position_count_bp.R
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@ -96,7 +96,7 @@ site_snp_count_bp <- function (plotdf
# but atm being using as plot title
#my_leg_title
bp_plot_title = paste0("Total nsSNPs: ", tot_muts
, ", Total no. of nsSNPs sites: ", tot_sites)
, "\nTotal sites: ", tot_sites)
#-------------
# start plot 2
@ -123,7 +123,8 @@ site_snp_count_bp <- function (plotdf
#, legend.text = element_text(size = leg_text_size)
#, legend.title = element_text(size = axis_label_size)
, plot.title = element_text(size = leg_text_size
, colour = title_colour)
, colour = title_colour
, hjust = 0.5)
, plot.subtitle = element_text(size = subtitle_size
, hjust = 0.5
, colour = subtitle_colour)) +

9
scripts/functions/stability_count_bp.R
View file

@ -30,7 +30,8 @@ stability_count_bp <- function(plotdf
, sts = 20
, subtitle_colour = "pink"
#, leg_position = c(0.73,0.8) # within plot area
, leg_position = "top"){
, leg_position = "top"
, bar_fill_values = c("#F8766D", "#00BFC4")){
# OutPlot_count = ggplot(plotdf, aes(x = eval(parse(text = df_colname)))) +
OutPlot_count = ggplot(plotdf, aes_string(x = df_colname)) +
@ -57,8 +58,10 @@ stability_count_bp <- function(plotdf
, subtitle = subtitle_text
, y = yaxis_title) +
scale_fill_discrete(name = leg_title
#, labels = c("Destabilising", "Stabilising")
, labels = label_categories)
, labels = label_categories) +
scale_fill_manual("", values=bar_fill_values)
return(OutPlot_count)
}