Skip to content

Commit

Permalink
Added more information about dependencies
Browse files Browse the repository at this point in the history
  • Loading branch information
@ChristinaSchmidt1
ChristinaSchmidt1 committed Oct 29, 2024
1 parent a653a47 commit a089a98
Showing 1 changed file with 20 additions and 17 deletions.
37 changes: 20 additions & 17 deletions R/VizSuperplots.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,9 @@
#'
#' @keywords Barplot, Boxplot, Violinplot, Superplot
#'
#' @importFrom ggplot2 ggplot theme
#' @importFrom ggplot2 ggplot theme geom_violin stat_summary geom_boxplot geom_bar labs scale_color_manual theme xlab ylab
#' @importFrom ggpubr stat_pvalue_manual
#' @importFrom grid convertUnit
#' @importFrom dplyr rename select group_by summarise_at filter mutate n
#' @importFrom magrittr %>% %<>%
#' @importFrom tibble rownames_to_column column_to_rownames
Expand All @@ -74,6 +76,11 @@ VizSuperplot <- function(InputData,
PrintPlot=TRUE,
FolderPath = NULL){

## ------------ Create log file ----------- ##
MetaProViz:::MetaProViz_Init()

logger::log_info("VizSuperplot: Superplot visualization")

## ------------ Check Input files ----------- ##
# HelperFunction `CheckInput`
MetaProViz:::CheckInput(InputData=InputData,
Expand Down Expand Up @@ -119,7 +126,6 @@ VizSuperplot <- function(InputData,
ColorPalette <- "grey"
}


## ------------ Check Input SettingsInfo ----------- ##
#7. Check StatComparisons & PlotConditions
if(is.null(PlotConditions)){
Expand Down Expand Up @@ -169,14 +175,12 @@ VizSuperplot <- function(InputData,
StatPadj <- "fdr"
}



## ------------ Create Results output folder ----------- ##
if(is.null(SaveAs_Plot)==FALSE){
Folder <- MetaProViz:::SavePath(FolderName= paste(PlotType, "Plots", sep=""),
FolderPath=FolderPath)
}

logger::log_info("VizSuperplot results saved at ", Folder)

###############################################################################################################################################################################################################
## ------------ Prepare Input ----------- ##
Expand Down Expand Up @@ -248,7 +252,7 @@ VizSuperplot <- function(InputData,
}

# Make the Plot
Plot <- ggplot(plotdata, aes(x = Conditions, y = Intensity))
Plot <- ggplot2::ggplot(plotdata, aes(x = Conditions, y = Intensity))

# Add graph style and error bar
data_summary <- function(x){#calculate error bar!
Expand All @@ -259,24 +263,24 @@ VizSuperplot <- function(InputData,
}

if (PlotType == "Bar"){
Plot <- Plot+ geom_bar(stat = "summary", fun = "mean", fill = ColorPalette)+ stat_summary(fun.data=data_summary,
Plot <- Plot+ ggplot2::geom_bar(stat = "summary", fun = "mean", fill = ColorPalette)+ ggplot2::stat_summary(fun.data=data_summary,
geom="errorbar", color="black", width=0.2)
} else if (PlotType == "Violin"){
Plot <- Plot+ geom_violin(fill = ColorPalette)+ stat_summary(fun.data=data_summary,
Plot <- Plot+ ggplot2::geom_violin(fill = ColorPalette)+ ggplot2::stat_summary(fun.data=data_summary,
geom="errorbar", color="black", width=0.2)
} else if (PlotType == "Box"){
Plot <- Plot + geom_boxplot(fill=ColorPalette, width=0.5, position=position_dodge(width = 0.5))
Plot <- Plot + ggplot2::geom_boxplot(fill=ColorPalette, width=0.5, position=position_dodge(width = 0.5))
}

# Add Superplot
if ("Superplot" %in% names(SettingsInfo)){
if(is.null(ColorPalette_Dot)==FALSE){
Plot <- Plot+ ggbeeswarm::geom_beeswarm(aes(x=Conditions,y=Intensity,color=as.factor(Superplot)),size=3)+
labs(color=SettingsInfo[["Superplot"]], fill = SettingsInfo[["Superplot"]])+
scale_color_manual(values = ColorPalette_Dot)
ggplot2::labs(color=SettingsInfo[["Superplot"]], fill = SettingsInfo[["Superplot"]])+
ggplot2::scale_color_manual(values = ColorPalette_Dot)
}else{
Plot <- Plot+ ggbeeswarm::geom_beeswarm(aes(x=Conditions,y=Intensity,color=as.factor(Superplot)),size=3)+
labs(color=SettingsInfo[["Superplot"]], fill = SettingsInfo[["Superplot"]])
ggplot2::labs(color=SettingsInfo[["Superplot"]], fill = SettingsInfo[["Superplot"]])
}
}else{
Plot <- Plot+ ggbeeswarm::geom_beeswarm(aes(x=Conditions,y=Intensity),size=2)
Expand All @@ -296,7 +300,7 @@ VizSuperplot <- function(InputData,
position = position_dodge(0.9), vjust = 0.25, show.legend = FALSE)

}
Plot <- Plot +labs(caption = paste("p.val using pairwise ", StatPval))
Plot <- Plot +ggplot2::labs(caption = paste("p.val using pairwise ", StatPval))
}else{
#All-vs-All comparisons table:
conditions <- SettingsFile_Sample$Conditions
Expand Down Expand Up @@ -359,17 +363,16 @@ VizSuperplot <- function(InputData,
}else{
Plot <- Plot +ggpubr::stat_pvalue_manual(df_merge, hide.ns = FALSE, size = 3, tip.length = 0.01, step.increase=0.01)#http://rpkgs.datanovia.com/ggpubr/reference/stat_pvalue_manual.html
}
Plot <- Plot +labs(caption = paste("p.adj using ", StatPval, "and", StatPadj))
Plot <- Plot +ggplot2::labs(caption = paste("p.adj using ", StatPval, "and", StatPadj))
}

Plot <- Plot + Theme+ labs(title = PlotName,
Plot <- Plot + Theme+ ggplot2::labs(title = PlotName,
subtitle = i)# ggtitle(paste(i))
Plot <- Plot + theme(legend.position = "right",plot.title = element_text(size=12, face = "bold"), axis.text.x = element_text(angle = 90, hjust = 1))+ xlab(xlab)+ ylab(ylab)
Plot <- Plot + ggplot2::theme(legend.position = "right",plot.title = element_text(size=12, face = "bold"), axis.text.x = element_text(angle = 90, hjust = 1))+ ggplot2::xlab(xlab)+ ggplot2::ylab(ylab)

## Store the plot in the 'plots' list
PlotList[[i]] <- Plot


# Make plot into nice format:
Plot_Sized <- MetaProViz:::plotGrob_Superplot(InputPlot=Plot, SettingsInfo=SettingsInfo, SettingsFile_Sample=SettingsFile_Sample, PlotName = PlotName, Subtitle = i, PlotType=PlotType)
PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
Expand Down

0 comments on commit a089a98

Please sign in to comment.