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This commit is contained in:
Tanushree Tunstall 2022-08-17 18:42:15 +01:00
parent cd9b1ad245
commit c9d7ea9fad
10 changed files with 208 additions and 128 deletions
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44
scripts/functions/logoP_or.R
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@ -81,13 +81,11 @@ LogoPlotCustomH <- function(plot_df
if (rm_empty_y){
cat(paste0("Original Rows: ",nrow(plot_df)))
plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
cat("\nRemoving empty positions...\n")
cat(paste0("Plotting Rows after removing NAs: ",nrow(plot_df)))
}
y_max = max(plot_df[[y_axis_colname]], na.rm = T)
cat("\nRemoving y scale incremenet:", y_axis_increment)
y_lim = round_any(y_max, y_axis_increment, f = ceiling)
#-------------------
# logo data: LogOR
@ -98,8 +96,10 @@ LogoPlotCustomH <- function(plot_df
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 = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, log_colname, fill = 0.0))
logo_df_plot = logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0)
rownames(logo_df_plot) = logo_df_plot$mutant_type
logo_df_plot$mutant_type = NULL
logo_dfP_wf=as.matrix(logo_df_plot)
#!!! For consideration: to add y_axis 'breaks' and 'limits' !!!
#y_max = max(plot_df[[log_colname]], na.rm = T)
#y_axis_increment =
@ -114,18 +114,28 @@ LogoPlotCustomH <- function(plot_df
#-------------------
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_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
logo_df_plot = logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0)
rownames(logo_df_plot) = logo_df_plot$mutant_type
logo_df_plot$mutant_type = NULL
logo_dfP_wf=as.matrix(logo_df_plot)
#logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
}
#class(logo_dfP_wf)
rownames(logo_dfP_wf) = logo_dfP_wf[,1]
#rownames(logo_dfP_wf) = logo_dfP_wf[,1]
#dim(logo_dfP_wf)
logo_dfP_wf = logo_dfP_wf[,-1]
#logo_dfP_wf = logo_dfP_wf[,-1]
#str(logo_dfP_wf)
#y_max = max(plot_df[[y_axis_colname]], na.rm = T)
y_max = max(colSums(logo_dfP_wf))
cat("\nRemoving y scale incremenet:", y_axis_increment)
y_lim = round_any(y_max, y_axis_increment, f = ceiling)
#colnames(logo_dfP_wf)
position_or = as.numeric(colnames(logo_dfP_wf))
@ -167,11 +177,12 @@ LogoPlotCustomH <- function(plot_df
ggplot() +
geom_logo(logo_dfP_wf
, method = "custom"
#, method = "bits"
, col_scheme = my_logo_col
, seq_type = "aa") +
#ylab("my custom height") +
theme( axis.ticks.x = element_blank()
, axis.ticks.length = unit(0, "pt")
theme( axis.ticks = element_blank()
#, axis.ticks.length = unit(0, "pt")
, axis.title.x = element_blank()
# , axis.text.x = element_blank() # turn this off and the below on if you want to visually
# verify positions.
@ -206,10 +217,13 @@ LogoPlotCustomH <- function(plot_df
, labels = position_or
, limits = factor(1:length(position_or))) +
scale_y_continuous(y_lab
, breaks = seq(0, (y_lim), by = y_axis_increment)
#, labels = seq(0, (y_lim), by = y_axis_increment)
, limits = c(0, y_lim)) +
scale_y_continuous(y_lab,
breaks = seq(0,
(y_lim),
by = y_axis_increment
),
limits = c(0, y_lim)
) +
labs(y=y_lab),
position_annotation(plot_df,
bg = theme_bgc,