adding legend forlogo plot
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4 changed files with 60 additions and 55 deletions
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@ -32,13 +32,15 @@
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#==================
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# NOTE: my_logo_col
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# Can be one of these: 'chemistry', 'hydrophobicity', 'clustalx', 'taylor'
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# if 'chemistry' or 'hydrophobicity' --> then bg is grey with black font
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# if 'clustalx'or 'taylor' --> then bg is black with white font
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# if 'chemistry' or 'hydrophobicity' --> then bg is grey with black font (x, y and labels)
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# if 'clustalx'or 'taylor' --> then bg is black with white font (x, y and labels)
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#, theme_bgc =
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#, xfont_bgc =
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#, yfont_bgc =
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#, xtt_col =
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#, ytt_col =
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# ADD legend for hydrophobicity
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# ADD legend for hydrophobicity: done
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# ADD option to remove empty positions
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LogoPlotCustomH <- function(plotdf
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@ -57,10 +59,12 @@ LogoPlotCustomH <- function(plotdf
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#, yfont_bgc
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, y_ats = 22
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, y_tangle = 0
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, x_tts = 25 # title size
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, y_tts = 20
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, leg_pos = "none"
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#, leg_pos = c(0.8, 0.9)
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, x_tts = 20 # title size
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, y_tts = 23
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#, xtt_col =
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#, ytt_col =
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, leg_pos = "none" # can be top, left, right and bottom or c(0.8, 0.9)
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, leg_dir = "horizontal" #can be vertical or horizontal
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, leg_ts = 15 # leg text size
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, leg_tts = 16 # leg title size
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)
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@ -72,13 +76,8 @@ LogoPlotCustomH <- function(plotdf
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logo_df = plotdf
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if (y_axis_log){
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log_colname = paste0("log_", y_axis_colname)
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logo_df[log_colname] = log_value(logo_df[y_axis_colname])
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}
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logo_data_plot2 = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
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logo_data_plot2 = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname, log_colname)]
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#==================
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# logo data: OR
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#==================
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@ -99,21 +98,26 @@ LogoPlotCustomH <- function(plotdf
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#==================
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# logo data: logOR
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#==================
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logo_data_plot2_logor = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
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wide_df2_logor = as.matrix(logo_data_plot2_logor %>% spread(x_axis_colname, log_colname, fill = 0.0))
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class(wide_df2_logor)
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rownames(wide_df2_logor) = wide_df2_logor[,1]
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dim(wide_df2_logor)
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#wide_df2_logor = subset(wide_df_logor, select = -c(1) )
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wide_df2_logor = wide_df2_logor[,-1]
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str(wide_df2_logor)
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colnames(wide_df2_logor)
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position_logor = as.numeric(colnames(wide_df2_logor))
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if (y_axis_log){
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log_colname = paste0("log_", y_axis_colname)
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logo_df[log_colname] = log_value(logo_df[y_axis_colname])
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logo_data_plot2 = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname,log_colname )]
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logo_data_plot2_logor = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
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wide_df2_logor = as.matrix(logo_data_plot2_logor %>% spread(x_axis_colname, log_colname, fill = 0.0))
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class(wide_df2_logor)
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rownames(wide_df2_logor) = wide_df2_logor[,1]
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dim(wide_df2_logor)
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wide_df2_logor = wide_df2_logor[,-1]
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str(wide_df2_logor)
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colnames(wide_df2_logor)
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position_logor = as.numeric(colnames(wide_df2_logor))
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}
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######################################
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# Generating plots with given y_axis
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@ -123,10 +127,11 @@ LogoPlotCustomH <- function(plotdf
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if (my_logo_col %in% c('clustalx','taylor')) {
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cat("\nSelected colour scheme:", my_logo_col
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, "\nUsing black theme\n")
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theme_bgc = "black"
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theme_bgc = "black"
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xfont_bgc = "white"
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yfont_bgc = "black"
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yfont_bgc = "white"
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xtt_col = "white"
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ytt_col = "white"
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}
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if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
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@ -135,7 +140,8 @@ LogoPlotCustomH <- function(plotdf
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theme_bgc = "grey"
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xfont_bgc = "black"
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yfont_bgc = "black"
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xtt_col = "black"
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ytt_col = "black"
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}
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LogoPlot = ggseqlogo(wide_df2_or
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@ -152,10 +158,12 @@ LogoPlotCustomH <- function(plotdf
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, hjust = 1
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, vjust = 0
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, colour = yfont_bgc)
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, axis.title.y = element_text(size = x_tts)
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, axis.title.x = element_text(size = y_tts)
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#, legend.position = "bottom") +
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc))+
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#, legend.text = element_text(size = leg_ts)
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#, legend.title = element_text(size = leg_tts))+
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@ -165,7 +173,6 @@ LogoPlotCustomH <- function(plotdf
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, limits = factor(1:length(position_or))) +
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ylab(y_lab)
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#print(logo_or)
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return(LogoPlot)
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}
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@ -7,21 +7,20 @@ LogoPlotCustomH (plotdf = merged_df3
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, x_axis_colname = "position"
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, y_axis_colname = "or_mychisq"
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, symbol_colname = "mutant_type"
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, y_axis_log = T
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, y_axis_log = F
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, log_value = log10
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, my_logo_col = 'hydrophobicity'
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#, theme_bgc
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# , xfont_bgc
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# , yfont_bgc
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, my_logo_col = 'chemistry'
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, x_lab = "Position"
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, y_lab = "Odds Ratio"
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, x_ats = 12 # text size
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, x_tangle = 90 # text angle
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, y_ats = 22
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, y_tangle = 0
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, x_tts = 25 # title size
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, y_tts = 20
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, leg_pos = "none"
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, x_tts = 20 # title size
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, y_tts = 23
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#, leg_pos = c(0.05,-0.12)
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, leg_pos = "top"
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, leg_dir = "horizontal"
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, leg_ts = 15 # leg text size
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, leg_tts = 16 # leg title size
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)
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@ -69,25 +69,25 @@ svg(plot_logo_or, width = 30 , height = 6)
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logo_or = ggseqlogo(wide_df_or
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, method = "custom"
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, seq_type = "aa") + ylab("my custom height") +
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theme( axis.text.x = element_text(size = 12
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, angle = 90
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theme( axis.text.x = element_text(size = x_ats
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, angle = x_tangle
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, hjust = 1
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, vjust = 0.4)
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, axis.text.y = element_text(size = 22
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, angle = 0
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, axis.text.y = element_text(size = y_ats
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, angle = y_tangle
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, hjust = 1
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, vjust = 0)
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, axis.title.y = element_text(size = 25)
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, axis.title.x = element_text(size = 20)
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, axis.title.y = element_text(size = x_tts)
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, axis.title.x = element_text(size = y_tts)
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#, legend.position = "bottom") +
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, legend.position = "none")+
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#, legend.text = element_text(size = 15)
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#, legend.title = element_text(size = 15))+
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scale_x_discrete("Position"
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, legend.position = leg_pos)+
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#, legend.text = element_text(size = leg_ts)
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#, legend.title = element_text(size = leg_tts))+
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scale_x_discrete(x_lab
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#, breaks
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, labels = position_or
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, limits = factor(1:length(position_or))) +
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ylab("Odds Ratio")
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ylab(y_lab)
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print(logo_or)
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#dev.off()
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@ -30,7 +30,6 @@ wc -l TEST2.csv
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sed -E 's/>.*//g' TEST2.csv | sed '/^$/d' > TEST3.csv
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wc -l TEST3.csv
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# doubles the no as it adds the mut info
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python3 mutate.py -v -o /home/tanu/git/LSHTM_analysis/scripts/plotting/scratch_plots/TEST.csv /home/tanu/git/LSHTM_analysis/scripts/plotting/scratch_plots/pnca_mut_map.csv /home/tanu/git/Data/pyrazinamide/input/pnca.fasta
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