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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,30 @@ | ||
| #' Runs correlation analysis pipeline | ||
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| #' @param dataset_name name of the dataset used to select significant DEGs from (specified as a string, name as in allstudies) | ||
| #' @param allstudies a list containing all the datasets (as SCE objects) | ||
| #' @param celltypes a list containing the celltypes to compute mean correlation across | ||
| #' @param pvals list of p-value cut-offs which will be used to select DEGs | ||
| #' @param data_names names of the datasets as they appear in the correlation plot | ||
| #' @param alphaval (alpha) transparency of the non-mean boxplots | ||
| #' @param numPerms number of random permutations of the dataset used to select significant DEGs from | ||
| #' @param numSubsets number of pairs of random subsets of the dataset used to select significant DEGs from | ||
| #' @param output_path base path in which outputs will be stored | ||
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| #' Saves all plots and DE outputs in the appropriate directories | ||
| #' @export | ||
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| correlation_analysis <- function(dataset_name="placeholder", | ||
| allstudies="placeholder", | ||
| celltypes="placeholder", | ||
| pvals=c(0.05,0.025,0.01,0.001,0.0001), | ||
| data_names="placeholder", | ||
| alphaval="placeholder", | ||
| numPerms="placeholder", | ||
| numSubsets="placeholder", | ||
| output_path=getwd()){ | ||
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| # create correlation plots for each p-value cut-off | ||
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| return("TestOut") | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,150 @@ | ||
| #' Tests input parameters for functions | ||
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| #' @param dataset_name name of the dataset used to select significant DEGs from (specified as a string, name as in allStudies) | ||
| #' @param allstudies a list containing all the datasets (most likely as SCE objects) | ||
| #' @param celltypes a list containing the celltypes to compute mean correlation across | ||
| #' @param pvalue the cut-off p-value which will be used to select DEGs | ||
| #' @param data_names names of the datasets as they appear in the correlation plot | ||
| #' @param corrMats (named) list of correlation matrices for each celltype with the final element being the mean correlation matrix, all at specified p-value | ||
| #' @param numRealDatasets total number of *real* datasets (most likely the number of studies, but sometimes a study may be split e.g. into 2 brain regions, so in this case it would be the number of studies plus 1) | ||
| #' @param alphaval (alpha) transparency of the non-mean boxplots | ||
| #' @param numPerms number of random permutations of the dataset used to select significant DEGs from | ||
| #' @param numSubsets number of pairs of random subsets of the dataset used to select significant DEGs from | ||
| #' @param sexDEGs true if DEGs come from sex chromosomes, else false | ||
| #' @param fontsize_yaxislabels font size for axis labels in plot | ||
| #' @param fontsize_yaxisticks font size for axis tick labels in plot | ||
| #' @param fontsize_title font size for plot title | ||
| #' @param fontsize_legendlabels font size for legend labels in plot | ||
| #' @param fontsize_legendtitle font size for legend title in plot | ||
| #' @param fontsize_facet_labels font size for facet labels | ||
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| #' Checks all correlation analysis parameters are specified correctly | ||
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| validate_input_parameters_correlation <- function(dataset_name="placeholder", | ||
| allstudies="placeholder", | ||
| celltypes="placeholder", | ||
| pvalue="placeholder", | ||
| data_names="placeholder", | ||
| corrMats="placeholder", | ||
| numRealDatasets="placeholder", | ||
| alphaval="placeholder", | ||
| numPerms="placeholder", | ||
| numSubsets="placeholder", | ||
| sexDEGs="placeholder", | ||
| fontsize_yaxislabels="placeholder", | ||
| fontsize_yaxisticks="placeholder", | ||
| fontsize_title="placeholder", | ||
| fontsize_legendlabels="placeholder", | ||
| fontsize_legendtitle="placeholder", | ||
| fontsize_facet_labels="placeholder"){ | ||
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| # test each parameter to check if it works | ||
| if(dataset_name!="placeholder"){ | ||
| if(!is.character(dataset_name)){ | ||
| stop("Error: dataset_name should be a string") | ||
| } | ||
| } | ||
| if(allstudies!="placeholder"){ | ||
| if(class(allstudies)!="list"){ | ||
| stop("Error: allstudies should be a list") | ||
| } | ||
| } | ||
| if(celltypes!="placeholder"){ | ||
| if(!is.character(celltypes)){ | ||
| stop("Error: celltypes should be a list containing strings specifying the celltypes") | ||
| } | ||
| } | ||
| if(pvalue!="placeholder"){ | ||
| if(!is.numeric(pvalue) | pvalue <= 0 | pvalue > 1){ | ||
| stop("Error: pvalue should be a (positive) number between 0 and 1") | ||
| } | ||
| } | ||
| if(data_names!="placeholder" && !is.vector(data_names)){ | ||
| stop("Error: data_names should be a list containing the names of all datasets as should appear in the final output (if these are different to the names in allstudies)") | ||
| } | ||
| if(corrMats!="placeholder"){ | ||
| if(class(corrMats)!="list"){ | ||
| stop("Error: corrMats should be a list of matrices") | ||
| } | ||
| } | ||
| if(numRealDatasets!="placeholder"){ | ||
| if(floor(numRealDatasets)!=numRealDatasets){ | ||
| stop("Error: numRealDatasets should be an integer specifying the number of real datasets (see description)") | ||
| } | ||
| } | ||
| if(alphaval!="placeholder"){ | ||
| if(class(alphaval)!="numeric"){ | ||
| stop("Error: alphaval should be numerical") | ||
| } | ||
| } | ||
| if(numPerms!="placeholder"){ | ||
| if(floor(numPerms)!=numPerms){ | ||
| stop("Error: numPerms should be an integer specifying the number of random permutations of Tsai (see description)") | ||
| } | ||
| } | ||
| if(numSubsets!="placeholder"){ | ||
| if(floor(numSubsets)!=numSubsets){ | ||
| stop("Error: numSubsets should be an integer specifying the number of subsets of Tsai (see description)") | ||
| } | ||
| } | ||
| if(sexDEGs!="placeholder"){ | ||
| if(class(sexDEGs)!="logical"){ | ||
| stop("Error: sexDEGs should be TRUE (if DEGs are chosen only from sex chromosomes) or FALSE") | ||
| } | ||
| } | ||
| if(fontsize_yaxislabels!="placeholder"){ | ||
| if(class(fontsize_yaxislabels)!="numeric"){ | ||
| stop("Error: fontsize_yaxislabels should be numerical") | ||
| }else{ | ||
| if(fontsize_yaxislabels-floor(fontsize_yaxislabels)!=0|fontsize_yaxislabels<0){ | ||
| stop("Error: fontsize_yaxislabels should be a positive integer") | ||
| } | ||
| } | ||
| } | ||
| if(fontsize_yaxisticks!="placeholder"){ | ||
| if(class(fontsize_yaxisticks)!="numeric"){ | ||
| stop("Error: fontsize_yaxisticks should be numerical") | ||
| }else{ | ||
| if(fontsize_yaxisticks-floor(fontsize_yaxisticks)!=0|fontsize_yaxisticks<0){ | ||
| stop("Error: fontsize_yaxisticks should be a positive integer") | ||
| } | ||
| } | ||
| } | ||
| if(fontsize_title!="placeholder"){ | ||
| if(class(fontsize_title)!="numeric"){ | ||
| stop("Error: fontsize_title should be numerical") | ||
| }else{ | ||
| if(fontsize_title-floor(fontsize_title)!=0|fontsize_title<0){ | ||
| stop("Error: fontsize_title should be a positive integer") | ||
| } | ||
| } | ||
| } | ||
| if(fontsize_legendlabels!="placeholder"){ | ||
| if(class(fontsize_legendlabels)!="numeric"){ | ||
| stop("Error: fontsize_legendlabels should be numerical") | ||
| }else{ | ||
| if(fontsize_legendlabels-floor(fontsize_legendlabels)!=0|fontsize_legendlabels<0){ | ||
| stop("Error: fontsize_legendlabels should be a positive integer") | ||
| } | ||
| } | ||
| } | ||
| if(fontsize_legendtitle!="placeholder"){ | ||
| if(class(fontsize_legendtitle)!="numeric"){ | ||
| stop("Error: fontsize_legendtitle should be numerical") | ||
| }else{ | ||
| if(fontsize_legendtitle-floor(fontsize_legendtitle)!=0|fontsize_legendtitle<0){ | ||
| stop("Error: fontsize_legendtitle should be a positive integer") | ||
| } | ||
| } | ||
| } | ||
| if(fontsize_facet_labels!="placeholder"){ | ||
| if(class(fontsize_facet_labels)!="numeric"){ | ||
| stop("Error: fontsize_facet_labels should be numerical") | ||
| }else{ | ||
| if(fontsize_facet_labels-floor(fontsize_facet_labels)!=0|fontsize_facet_labels<0){ | ||
| stop("Error: fontsize_facet_labels should be a positive integer") | ||
| } | ||
| } | ||
| } | ||
|
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||
| } |
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