saving logoplot attempts

meta_data_analysis/run_mutate.sh

@@ -1,8 +1,15 @@
 #!/bin/bash
 
+#https://www.biostars.org/p/336891/
+#python Mutate.py -v -o /path/to/output.fasta mutation_map_file.csv input.fasta
+
+# pnca_all_muts_msa_FIXME: This should be formatted like this from python script
+# change to a cmd script that takes this "prefix" as an input
+for i in $(cat pnca_all_muts_msa_FIXME.csv); do echo "3PL1,${i}"; done > pnca_copy.txt
+
 # make sure there is no new line at the end of the mutation file (snps.csv)
 #python3 Mutate.py -v -o /home/tanu/git/Data/pyrazinamide/input/output.fasta mut_map.csv 3pl1.fasta.txt
-python3 mutate.py -v -o /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt /home/tanu/git/Data/pyrazinamide/output/pnca_all_muts_msa.csv /home/tanu/git/Data/pyrazinamide/input/3pl1.fasta.txt
+python3 mutate.py -v -o /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt /home/tanu/git/Data/pyrazinamide/output/pnca_all_muts_msa.csv /home/tanu/git/Data/pyrazinamide/input/pnca_fasta.txt
 
 # remove fasta style header lines in the output i.e
 # lines beginning with '>' so the file is just the mutated seqs

scripts/plotting/Header_TT.R

@@ -139,3 +139,5 @@ if(!require(bio3d)){
   library(bio3d)
 }
 
+#install.packages("protr")
+library(protr)

scripts/plotting/logo_plot.R

@@ -57,12 +57,13 @@ plot_logo_plot = paste0(plotdir,"/", logo_plot)
 # REASSIGNMENT
 #my_data = merged_df2
 #my_data =  merged_df2_comp
-#my_data = merged_df3
+my_data = merged_df3
 my_data = merged_df3_comp
 #%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 # delete variables not required
-rm(merged_df2, merged_df2_comp, merged_df3, merged_df3_comp)
+rm(merged_df2, merged_df2_comp)
+#rm(merged_df3, merged_df3_comp)
 
 # quick checks
 colnames(my_data)
@@ -107,40 +108,63 @@ foo = my_data_snp[, c("position", "mutant_type","duet_scaled", "or_mychisq"
                       , "mut_prop_polarity", "mut_prop_water") ] 
 
 my_data_snp$log10or = log10(my_data_snp$or_mychisq)
-bar = my_data_snp[, c("position", "mutant_type", "or_mychisq", "log10or")]
+logo_data = my_data_snp[, c("position", "mutant_type", "or_mychisq", "log10or")]
+
+logo_data_or = my_data_snp[, c("position", "mutant_type", "or_mychisq")]
+wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
 
-bar_or = my_data_snp[, c("position", "mutant_type", "or_mychisq")]
-wide_df_or <- bar_or %>% spread(position, or_mychisq, fill = 0)
 wide_df_or = as.matrix(wide_df_or)
 rownames(wide_df_or) = wide_df_or[,1]
 wide_df_or = wide_df_or[,-1]
 
+position_or = as.numeric(colnames(wide_df_or))
+
+#===========================================
+#custom height (OR) logo plot: CORRECT x-axis labelling
+#============================================  
 # custom height (OR) logo plot: yayy works
+
 ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custom height") +
-  theme(legend.position = "bottom"
+    theme(legend.position = "bottom"
-        , axis.text.x = element_text(size = 11
+          , axis.text.x = element_text(size = 11
-                                     , angle = 90
+                                       , angle = 90
-                                     , hjust = 1
+                                       , hjust = 1
-                                     , vjust = 0.4)
+                                       , vjust = 0.4)
-        , axis.text.y = element_text(size = 15
+          , axis.text.y = element_text(size = 15
-                                     , angle = 0
+                                       , angle = 0
-                                     , hjust = 1
+                                       , hjust = 1
-                                     , vjust = 0))+
+                                       , vjust = 0))+
-  labs(title = "AA logo plot"
+    scale_x_discrete("Position"
-       , x = "Wild-type position"
+                     #, breaks
-       , y = "OR")
+                     , labels = position_or
+                     , limits = factor(1:length(position_or))) +
+  ylab("Odds Ratio")
+  
 #%% end of logo plot with OR as height
+
 #=======================================================================
 # extracting data with log10R
-bar_logor = my_data_snp[, c("position", "mutant_type", "log10or")]
+logo_data_logor = my_data_snp[, c("position", "mutant_type", "log10or")]
-wide_df_logor <- bar_logor %>% spread(position, log10or, fill = 0)
+wide_df_logor <- logo_data_logor %>% spread(position, log10or, fill = 0.0)
 
 wide_df_logor = as.matrix(wide_df_logor)
+
 rownames(wide_df_logor) = wide_df_logor[,1]
-wide_df_logor = wide_df_logor[,-1]
+wide_df_logor = subset(wide_df_logor, select = -c(1) )
+colnames(wide_df_logor)
+wide_df_logor_m = data.matrix(wide_df_logor)
+
+rownames(wide_df_logor_m)
+colnames(wide_df_logor_m)
+
+# FIXME
+#my_ylim_up = as.numeric(max(wide_df_logor_m)) * 5
+#my_ylim_low = as.numeric(min(wide_df_logor_m))
+
+position_logor = as.numeric(colnames(wide_df_logor_m))
 
 #  custom height (log10OR) logo plot: yayy works
-ggseqlogo(wide_df_logor, method="custom", seq_type="aa") + ylab("my custom height") +
+ggseqlogo(wide_df_logor_m, method="custom", seq_type="aa") + ylab("my custom height") +
   theme(legend.position = "bottom"
         , axis.text.x = element_text(size = 11
                                      , angle = 90
@@ -150,9 +174,12 @@ ggseqlogo(wide_df_logor, method="custom", seq_type="aa") + ylab("my custom heigh
                                      , angle = 0
                                      , hjust = 1
                                      , vjust = 0))+
-  labs(title = "AA logo plot"
+  scale_x_discrete("Position"
-       , x = "Wild-type position"
+                   #, breaks
-       , y = "Log10(OR)")
+                   , labels = position_logor
+                   , limits = factor(1:length(position_logor)))+
+  ylab("Log (Odds Ratio)") + 
+  scale_y_continuous(limits = c(0, 9))
 
 #=======================================================================
 #%% logo plot from sequence
@@ -167,7 +194,7 @@ library(Logolas)
 # data was pnca_msa.txt
 #FIXME: generate this file 
 
-seqs = read.csv("~/git//Data/pyrazinamide/snp_seqsfile.txt"
+seqs = read.csv("~/git/Data/pyrazinamide/output/pnca_msa.txt"
                 , header = FALSE
                 , stringsAsFactors = FALSE)$V1
 
@@ -175,7 +202,63 @@ seqs = read.csv("~/git//Data/pyrazinamide/snp_seqsfile.txt"
 # my_data: useful!
 logomaker(seqs, type = "EDLogo", color_type = "per_symbol"
           , return_heights = TRUE)
-logomaker(seqs, type = "Logo", color_type = "per_symbol")
+
+logomaker(seqs, type = "Logo", color_type = "per_symbol", return_heights = TRUE)
 
 #%% end of script
 #=======================================================================
+#==============
+# online logo:
+#http://www.cbs.dtu.dk/biotools/Seq2Logo/ # good for getting pssm and psfm matrices
+#https://weblogo.berkeley.edu/logo.cgi
+#http://weblogo.threeplusone.com/create.cgi   # weblogo3
+
+#===============
+# PSSM logos= example from logomaker
+#===============
+
+data(pssm)
+logo_pssm(pssm, control = list(round_off = 0))
+
+#=================
+# PSSM: output from http://www.cbs.dtu.dk/biotools/Seq2Logo/
+# of MSA: pnca_msa.txt
+#==================
+foo = read.csv("/home/tanu/git/Data/pyrazinamide/pssm_transpose.csv")
+rownames(foo) = foo[,1]
+df = subset(foo, select = -c(1) )
+colnames(df)
+colnames(df) = seq(1:length(df))
+
+df_m = as.matrix(df)
+logo_pssm(df_m, control = list(round_off = 0))
+
+#=================
+# # PSFM: output from http://www.cbs.dtu.dk/biotools/Seq2Logo/
+# of MSA: pnca_msa.txt
+#=================
+# not designed for PSFM!
+# may want to figure out how to do it!
+logo_data = read.csv("/home/tanu/git/Data/pyrazinamide/psfm_transpose.csv")
+rownames(logo_data) = logo_data[,1]
+df2 = subset(logo_data, select = -c(1) )
+colnames(df2)
+colnames(df2) = seq(1:length(df2))
+
+df2_m = as.matrix(df2)
+logo_pssm(df2_m, control = list(round_off = 0))
+
+
+#=================
+# ggplots:
+#https://stackoverflow.com/questions/5438474/plotting-a-sequence-logo-using-ggplot2
+#=================
+
+library(ggplot2)
+library(gglogo)
+ggplot(data = ggfortify(sequences, "peptide")) +      
+  geom_logo(aes(x=position, y=bits, group=element, 
+                label=element, fill=interaction(Polarity, Water)),
+            alpha = 0.6)  +
+  scale_fill_brewer(palette="Paired") +
+  theme(legend.position = "bottom")