saving logoplot attempts
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3 changed files with 119 additions and 27 deletions
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@ -57,12 +57,13 @@ plot_logo_plot = paste0(plotdir,"/", logo_plot)
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# REASSIGNMENT
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#my_data = merged_df2
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#my_data = merged_df2_comp
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#my_data = merged_df3
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my_data = merged_df3
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my_data = merged_df3_comp
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#%%%%%%%%%%%%%%%%%%%%%%%%%%
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# delete variables not required
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rm(merged_df2, merged_df2_comp, merged_df3, merged_df3_comp)
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rm(merged_df2, merged_df2_comp)
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#rm(merged_df3, merged_df3_comp)
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# quick checks
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colnames(my_data)
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@ -107,40 +108,63 @@ foo = my_data_snp[, c("position", "mutant_type","duet_scaled", "or_mychisq"
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, "mut_prop_polarity", "mut_prop_water") ]
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my_data_snp$log10or = log10(my_data_snp$or_mychisq)
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bar = my_data_snp[, c("position", "mutant_type", "or_mychisq", "log10or")]
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logo_data = my_data_snp[, c("position", "mutant_type", "or_mychisq", "log10or")]
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logo_data_or = my_data_snp[, c("position", "mutant_type", "or_mychisq")]
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wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
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bar_or = my_data_snp[, c("position", "mutant_type", "or_mychisq")]
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wide_df_or <- bar_or %>% spread(position, or_mychisq, fill = 0)
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wide_df_or = as.matrix(wide_df_or)
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rownames(wide_df_or) = wide_df_or[,1]
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wide_df_or = wide_df_or[,-1]
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position_or = as.numeric(colnames(wide_df_or))
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#===========================================
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#custom height (OR) logo plot: CORRECT x-axis labelling
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#============================================
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# custom height (OR) logo plot: yayy works
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ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custom height") +
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theme(legend.position = "bottom"
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, axis.text.x = element_text(size = 11
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, angle = 90
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, hjust = 1
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, vjust = 0.4)
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, axis.text.y = element_text(size = 15
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, angle = 0
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, hjust = 1
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, vjust = 0))+
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labs(title = "AA logo plot"
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, x = "Wild-type position"
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, y = "OR")
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theme(legend.position = "bottom"
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, axis.text.x = element_text(size = 11
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, angle = 90
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, hjust = 1
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, vjust = 0.4)
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, axis.text.y = element_text(size = 15
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, angle = 0
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, hjust = 1
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, vjust = 0))+
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scale_x_discrete("Position"
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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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#%% end of logo plot with OR as height
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#=======================================================================
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# extracting data with log10R
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bar_logor = my_data_snp[, c("position", "mutant_type", "log10or")]
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wide_df_logor <- bar_logor %>% spread(position, log10or, fill = 0)
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logo_data_logor = my_data_snp[, c("position", "mutant_type", "log10or")]
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wide_df_logor <- logo_data_logor %>% spread(position, log10or, fill = 0.0)
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wide_df_logor = as.matrix(wide_df_logor)
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rownames(wide_df_logor) = wide_df_logor[,1]
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wide_df_logor = wide_df_logor[,-1]
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wide_df_logor = subset(wide_df_logor, select = -c(1) )
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colnames(wide_df_logor)
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wide_df_logor_m = data.matrix(wide_df_logor)
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rownames(wide_df_logor_m)
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colnames(wide_df_logor_m)
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# FIXME
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#my_ylim_up = as.numeric(max(wide_df_logor_m)) * 5
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#my_ylim_low = as.numeric(min(wide_df_logor_m))
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position_logor = as.numeric(colnames(wide_df_logor_m))
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# custom height (log10OR) logo plot: yayy works
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ggseqlogo(wide_df_logor, method="custom", seq_type="aa") + ylab("my custom height") +
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ggseqlogo(wide_df_logor_m, method="custom", seq_type="aa") + ylab("my custom height") +
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theme(legend.position = "bottom"
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, axis.text.x = element_text(size = 11
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, angle = 90
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@ -150,9 +174,12 @@ ggseqlogo(wide_df_logor, method="custom", seq_type="aa") + ylab("my custom heigh
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, angle = 0
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, hjust = 1
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, vjust = 0))+
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labs(title = "AA logo plot"
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, x = "Wild-type position"
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, y = "Log10(OR)")
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scale_x_discrete("Position"
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#, breaks
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, labels = position_logor
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, limits = factor(1:length(position_logor)))+
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ylab("Log (Odds Ratio)") +
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scale_y_continuous(limits = c(0, 9))
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#=======================================================================
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#%% logo plot from sequence
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@ -167,7 +194,7 @@ library(Logolas)
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# data was pnca_msa.txt
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#FIXME: generate this file
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seqs = read.csv("~/git//Data/pyrazinamide/snp_seqsfile.txt"
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seqs = read.csv("~/git/Data/pyrazinamide/output/pnca_msa.txt"
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, header = FALSE
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, stringsAsFactors = FALSE)$V1
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@ -175,7 +202,63 @@ seqs = read.csv("~/git//Data/pyrazinamide/snp_seqsfile.txt"
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# my_data: useful!
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logomaker(seqs, type = "EDLogo", color_type = "per_symbol"
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, return_heights = TRUE)
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logomaker(seqs, type = "Logo", color_type = "per_symbol")
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logomaker(seqs, type = "Logo", color_type = "per_symbol", return_heights = TRUE)
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#%% end of script
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#=======================================================================
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#==============
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# online logo:
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#http://www.cbs.dtu.dk/biotools/Seq2Logo/ # good for getting pssm and psfm matrices
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#https://weblogo.berkeley.edu/logo.cgi
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#http://weblogo.threeplusone.com/create.cgi # weblogo3
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#===============
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# PSSM logos= example from logomaker
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#===============
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data(pssm)
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logo_pssm(pssm, control = list(round_off = 0))
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#=================
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# PSSM: output from http://www.cbs.dtu.dk/biotools/Seq2Logo/
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# of MSA: pnca_msa.txt
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#==================
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foo = read.csv("/home/tanu/git/Data/pyrazinamide/pssm_transpose.csv")
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rownames(foo) = foo[,1]
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df = subset(foo, select = -c(1) )
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colnames(df)
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colnames(df) = seq(1:length(df))
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df_m = as.matrix(df)
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logo_pssm(df_m, control = list(round_off = 0))
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#=================
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# # PSFM: output from http://www.cbs.dtu.dk/biotools/Seq2Logo/
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# of MSA: pnca_msa.txt
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#=================
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# not designed for PSFM!
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# may want to figure out how to do it!
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logo_data = read.csv("/home/tanu/git/Data/pyrazinamide/psfm_transpose.csv")
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rownames(logo_data) = logo_data[,1]
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df2 = subset(logo_data, select = -c(1) )
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colnames(df2)
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colnames(df2) = seq(1:length(df2))
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df2_m = as.matrix(df2)
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logo_pssm(df2_m, control = list(round_off = 0))
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#=================
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# ggplots:
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#https://stackoverflow.com/questions/5438474/plotting-a-sequence-logo-using-ggplot2
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#=================
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library(ggplot2)
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library(gglogo)
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ggplot(data = ggfortify(sequences, "peptide")) +
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geom_logo(aes(x=position, y=bits, group=element,
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label=element, fill=interaction(Polarity, Water)),
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alpha = 0.6) +
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scale_fill_brewer(palette="Paired") +
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theme(legend.position = "bottom")
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