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added option to remove empty positions from logo plot

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This commit is contained in:
Tanushree Tunstall 2022-01-14 11:07:16 +00:00
parent 4e2f5f35db
commit f27b536157
2 changed files with 21 additions and 15 deletions
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33
scripts/functions/logo_plots_func.R
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@ -49,6 +49,7 @@ LogoPlotCustomH <- function(plot_df
, symbol_colname = "mutant_type" , symbol_colname = "mutant_type"
, y_axis_log = F , y_axis_log = F
, log_value = log10 , log_value = log10
, rm_empty_pos = F
, my_logo_col = "chemistry" , my_logo_col = "chemistry"
, x_lab = "Position" , x_lab = "Position"
, y_lab = "Odds Ratio" , y_lab = "Odds Ratio"
@ -70,14 +71,20 @@ LogoPlotCustomH <- function(plot_df
) )
{ {
################################# #################################
# Data processing for logo plot # Data processing for logo plot
################################# #################################
if (y_axis_log){ if (rm_empty_pos){
plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
#===================== cat("\nRemoving empty positions...\n")
}else{
plot_df = plot_df
}
#-------------------
# logo data: LogOR # logo data: LogOR
#===================== #-------------------
if (y_axis_log){
log_colname = paste0("log_", y_axis_colname) log_colname = paste0("log_", y_axis_colname)
plot_df[log_colname] = log_value(plot_df[y_axis_colname]) plot_df[log_colname] = log_value(plot_df[y_axis_colname])
logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)] logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)]
@ -86,9 +93,9 @@ LogoPlotCustomH <- function(plot_df
} else { } else {
#===================== #-------------------
# logo data: OR # logo data: OR
#===================== #-------------------
logo_df = plot_df[, c(x_axis_colname, symbol_colname, y_axis_colname)] logo_df = plot_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)] logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0)) logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
@ -109,11 +116,10 @@ LogoPlotCustomH <- function(plot_df
###################################### ######################################
# Generating plots with given y_axis # Generating plots with given y_axis
##################################### #####################################
#if (my_logo_col == 'clustalx || taylor'){
if (my_logo_col %in% c('clustalx','taylor')) { if (my_logo_col %in% c('clustalx','taylor')) {
cat("\nSelected colour scheme:", my_logo_col cat("\nSelected colour scheme:", my_logo_col
, "\nUsing black theme\n") , "\nUsing black theme\n")
theme_bgc = "black" theme_bgc = "black"
xfont_bgc = "white" xfont_bgc = "white"
yfont_bgc = "white" yfont_bgc = "white"
@ -124,6 +130,7 @@ LogoPlotCustomH <- function(plot_df
if (my_logo_col %in% c('chemistry', 'hydrophobicity')) { if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
cat('\nSelected colour scheme:', my_logo_col cat('\nSelected colour scheme:', my_logo_col
, "\nUsing grey theme") , "\nUsing grey theme")
theme_bgc = "grey" theme_bgc = "grey"
xfont_bgc = "black" xfont_bgc = "black"
yfont_bgc = "black" yfont_bgc = "black"
@ -162,6 +169,4 @@ LogoPlotCustomH <- function(plot_df
return(LogoPlot) return(LogoPlot)
} }

3
scripts/functions/tests/test_logo_plots_func.R
View file

@ -9,7 +9,8 @@ LogoPlotCustomH (plot_df = merged_df3
, symbol_colname = "mutant_type" , symbol_colname = "mutant_type"
, y_axis_log = F , y_axis_log = F
, log_value = log10 , log_value = log10
, my_logo_col = 'taylor' , rm_empty_pos = F
, my_logo_col = 'hydrophobicity'
, x_lab = "Position" , x_lab = "Position"
, y_lab = "Odds Ratio" , y_lab = "Odds Ratio"
, x_ats = 12 # text size , x_ats = 12 # text size