diff --git a/DESCRIPTION b/DESCRIPTION
index c0a519a..1431fd8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: gencoreBulk
Title: NPRC Genomics Core Bulk RNA Analysis Utilities
-Version: 0.2.2
+Version: 0.2.3
Date: 2024-03-22
Author: person("Derrik", "Gratz", email = "derrik.gratz@gmail.com", role =
c("aut", "cre"), comment = c(ORCID = "0009-0002-5934-576X"))
diff --git a/NAMESPACE b/NAMESPACE
index 0585539..f2e8962 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -22,6 +22,7 @@ export(plotFilterByExpr)
export(plotGeneExpression)
export(plotPCAFromConfig)
export(plotVoomByGroup)
+export(read_excel_allsheets)
export(runfgsea)
export(voomByGroup)
export(writeCountTables)
diff --git a/R/PCA.R b/R/PCA.R
index 286b48e..241508c 100644
--- a/R/PCA.R
+++ b/R/PCA.R
@@ -117,7 +117,7 @@ plotPCAFromConfig <- function(analysis,
#' }
#'
pcaPlotSimple <- function(counts, metadata, xpc = 1, ypc = 2, ntop = 500) {
- if (colnames(counts) != rownames(metadata)) {
+ if (all(colnames(counts) != rownames(metadata))) {
stop('Colnames of counts does not match rownames of metadata')
}
rv <- matrixStats::rowVars(counts)
diff --git a/R/gseaDotplot.R b/R/gseaDotplot.R
new file mode 100644
index 0000000..38f362b
--- /dev/null
+++ b/R/gseaDotplot.R
@@ -0,0 +1,238 @@
+#' GSEA dotplot for multiple contrasts
+#'
+#' Make dotplot from fGSEA result, showing top n pathways
+#'
+#' @rdname gseaDotplot_joint
+#'
+#' @param gsea_results A table with multiple GSEA results from `fgsea::fgseaSimple()`
+#' combined by `combine_GSEA_results()`
+#' @param pathway_order Order of pathways to plot
+#' @param x_order Order of comparisons on X axis
+#' @param significance A vector of values to indicate significance with asterisks.
+#' Each subsequent value will add an extra asterisk. E.g. `c(0.05, 0.01)` will
+#' give one asteriks to values below 0.05 and two asterisks to values below 0.01.
+#' If this is null, no asterisks will be plotted.
+#' @param p_val_col Column to use for significance values. Default 'pval'.
+#' @inheritParams ggplot2::scale_radius
+#'
+#' @return A ggplot object
+#' @export
+#'
+#' @importFrom rlang .data
+#' @import ggplot2
+#' @import dplyr
+#'
+#' @examples
+#' \dontrun{
+#' combine_GSEA_results <- function(gsea_results,
+#' pathways){
+#' gsea_results <- lapply(gsea_results, function(x){x %>% filter(pathway %in% pathways)})
+#' gsea_results <- data.table::rbindlist(gsea_results, idcol='ID')
+#' }
+#'
+#' pathways = c('REACTOME_SIGNALING_BY_GPCR', 'REACTOME_SIGNALING_BY_NTRKS')
+#' gsea_results <- list('FAC vs Cont' = gsea_result, 'LiproxposFAC vs Cont' = gsea_result_2)
+#' joint_GSEA_results <- combine_GSEA_results(gsea_results, pathways)
+#' gseaDotplot_joint(joint_GSEA_results)
+#' }
+gseaDotplot_joint <- function(gsea_results,
+ pathway_order = NULL,
+ x_order = NULL,
+ significance = c(0.05, 0.01, 0.001),
+ range = c(1,8),
+ breaks = -log10(c(0.1,0.01,0.001,0.0001)),
+ labels = c(0.1,0.01,0.001,0.0001),
+ p_val_col = 'pval'){
+ if (!is.null(pathway_order)) {
+ if (all(pathway_order %in% unique(gsea_results$pathway))){
+ pathway_order <- order(factor(gsea_results$pathway, levels = pathway_order))
+ gsea_results$pathway <- .wrap_underscore_strings_balance(gsea_results$pathway,36)
+ ## reordering
+ gsea_results <- gsea_results[pathway_order,]
+ gsea_results$pathway <- factor(gsea_results$pathway, levels = unique(gsea_results$pathway))
+ } else {
+ warning('pathways specified in pathway_order not found, defaulting to arbitrary order')
+ }
+ } else {
+ gsea_results$pathway <- .wrap_underscore_strings_balance(gsea_results$pathway,36)
+ }
+
+ if (!is.null(x_order)) {
+ if (all(x_order %in% unique(gsea_results$ID))){
+ gsea_results$ID <- factor(gsea_results$ID, levels = x_order)
+ } else {
+ warning('Specified x_order not all found in data, defaulting to arbitrary order')
+ }
+ }
+
+ gsea_results$label <- NA
+ caption <- ''
+ if (!is.null(significance)) {
+ if (is.numeric(significance)) {
+ label <- '*'
+ for (cutoff in significance) {
+ gsea_results$label <- ifelse(gsea_results[[p_val_col]] < cutoff, label, gsea_results$label)
+ caption <- paste(caption, label, '<', cutoff, ';', sep = ' ')
+ label <- paste0(label, '*')
+ }
+ # gsea_results$label[is.numeric(gsea_results$label)] <- NA
+ } else {
+ stop('Significance argument should be a numeric vector')
+ }
+ }
+ ggplot(gsea_results, aes(x=.data$ID, y=.data$pathway, size=-log(.data[[p_val_col]]),
+ color=.data$NES, label = .data$label)) +
+ geom_point() +
+ scale_color_gradient2(low="blue",
+ mid="white",
+ high="red",
+ midpoint=0,
+ breaks=c(-2,-1,0,1,2),
+ limits=c(min(gsea_results$NES,-1),
+ max(gsea_results$NES,1))) +
+ theme_classic(11) +
+ theme(panel.grid.major = element_line(colour = "grey92"),
+ panel.grid.minor = element_line(colour = "grey92"),
+ panel.grid.major.y = element_line(colour = "grey92"),#element_blank(),
+ panel.grid.minor.y = element_line(colour = "grey92")) +
+ theme(axis.text.x = element_text(angle = 90,
+ vjust = 0.5,
+ hjust=1)) +
+ labs(x="Comparison",
+ y="Gene set",
+ color = "Normalized\nenrichment\nscore",
+ size="Nom p-val",
+ title="GSEA pathway enrichments",
+ caption = caption) +
+ scale_radius(name="NOM p-val",
+ range=range,
+ breaks=breaks,
+ labels=labels) +
+ geom_text(na.rm = TRUE, color = 'white', size = 3)
+}
+
+#' GSEA dotplot for a single contrast
+#'
+#' Make dotplot from an fGSEA result, showing top n pathways
+#'
+#' @rdname gseaDotplot_single
+#' @param result A table with GSEA results from `fgsea::fgseaSimple()`
+#' @param min_size Minimum size of gene set to plot
+#' @param filter_source Character vector of pathway sources to filter for
+#' @param signif_only If TRUE, only plot results with p value < `sig_cutoff`
+#' @param top_n Show the top N results sorted by pval
+#' @param sig_cutoff Threshold for significance, default to 0.05
+#' @param significance A vector of values to indicate significance with asterisks.
+#' Each subsequent value will add an extra asterisk. E.g. `c(0.05, 0.01)` will
+#' give one asteriks to values below 0.05 and two asterisks to values below 0.01.
+#' If this is null, no asterisks will be plotted.
+#' @param use_shortened_pathway_names Pull names from column 'pathway_short'
+#' rather than pathway (if `runfgsea()` call had `breakdown_pathway_names` set
+#' to `TRUE`)
+#' @param p_val_col Column to use for significance values. Default 'pval'.
+#' @inheritParams ggplot2::scale_radius
+#'
+#' @return A ggplot object
+#' @export
+#'
+#' @importFrom rlang .data
+#' @importFrom utils head
+#' @import ggplot2
+#' @import dplyr
+#'
+#' @examples
+#' \dontrun{
+#' res <- runfgsea(result, gmt.file)
+#' gseaDotplot(res, filter_source = "HALLMARK")
+#' }
+gseaDotplot_single <- function(result,
+ filter_source = NULL,
+ signif_only = FALSE,
+ top_n = 20,
+ min_size = 5,
+ sig_cutoff = 0.05,
+ use_shortened_pathway_names = FALSE,
+ significance = c(0.05, 0.01, 0.001),
+ range = c(1,8),
+ breaks = -log10(c(0.1,0.01,0.001,0.0001)),
+ labels = c(0.1,0.01,0.001,0.0001),
+ p_val_col = 'pval') {
+ if (use_shortened_pathway_names){
+ result$pathway <- result$pathway_short
+ }
+ result <- result %>%
+ arrange(.data[[p_val_col]], desc(.data$NES)) %>%
+ mutate(perc = 100 * lengths(.data$leadingEdge) / .data$size) %>%
+ mutate(name = paste0(.wrap_underscore_strings_balance(.data$pathway, 36), "\nn=", .data$size)) %>%
+ filter(.data$size >= min_size)
+ if (!is.null(filter_source)) {
+ result <- result %>%
+ filter(.data$source %in% filter_source)
+ }
+ if (signif_only) {
+ result <- result %>%
+ filter(.data[[p_val_col]] < sig_cutoff)
+ }
+
+ result$label <- NA
+ caption <- ''
+ if (!is.null(significance)) {
+ if (is.numeric(significance)) {
+ label <- '*'
+ for (cutoff in significance) {
+ result$label <- ifelse(result$pval < cutoff, label, result$label)
+ caption <- paste(caption, label, '<', cutoff, ';', sep = ' ')
+ label <- paste0(label, '*')
+ }
+ # gsea_results$label[is.numeric(gsea_results$label)] <- NA
+ } else {
+ stop('Significance argument should be a numeric vector')
+ }
+ }
+
+
+ toppaths <- rbind(utils::head(result, n = top_n))
+ toppaths$name <- factor(toppaths$name)
+ dotplot <- ggplot(toppaths,
+ aes(
+ x = .data[['perc']],
+ y = .data[['name']],
+ size = -log10(.data[['pval']]),
+ color = .data[['NES']],
+ label = .data[['label']])) +
+ geom_point() +
+ scale_color_gradient2(
+ low = "blue",
+ mid = "white",
+ high = "red",
+ midpoint = 0,
+ breaks = c(-2, -1, 0, 1, 2),
+ limits = c(
+ min(toppaths$NES, -1),
+ max(toppaths$NES, 1)
+ )
+ ) +
+ theme_classic(11) +
+ theme(
+ panel.grid.major = element_line(colour = "grey92"),
+ panel.grid.minor = element_line(colour = "grey92"),
+ panel.grid.major.y = element_line(colour = "grey92"),
+ panel.grid.minor.y = element_line(colour = "grey92")
+ ) +
+ theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +
+ labs(
+ x = "% of genes in leading edge", y = "Gene set",
+ color = "Normalized\nenrichment\nscore",
+ size = "Nom p-val", title = "Top enriched pathways",
+ caption = paste0("n = number of genes in pathway\n", caption)) +
+ scale_radius(
+ name = "NOM p-val",
+ range = range,
+ breaks = breaks,
+ # limits = c(0, 3),
+ labels = labels
+ ) +
+ scale_y_discrete(limits = toppaths$name) +
+ geom_text(na.rm = TRUE, color = 'white', size = 3)
+ return(dotplot)
+}
diff --git a/R/gseaDotplot_joint.R b/R/gseaDotplot_joint.R
deleted file mode 100644
index 28f3f19..0000000
--- a/R/gseaDotplot_joint.R
+++ /dev/null
@@ -1,108 +0,0 @@
-#' GSEA dotplot
-#'
-#' Make dotplot from fGSEA result, showing top n pathways
-#'
-#' @rdname gseaDotplot_joint
-#'
-#' @param gsea_results A table with multiple GSEA results from `fgsea::fgseaSimple()`
-#' combined by `combine_GSEA_results()`
-#' @param pathway_order Order of pathways to plot
-#' @param x_order Order of comparisons on X axis
-#' @param significance A vector of values to indicate significance with asterisks.
-#' Each subsequent value will add an extra asterisk. E.g. `c(0.05, 0.01)` will
-#' give one asteriks to values below 0.05 and two asterisks to values below 0.01.
-#' If this is null, no asterisks will be plotted.
-#' @param p_val_col Column to use for significance values. Default 'pval'.
-#'
-#' @return A ggplot object
-#' @export
-#'
-#' @importFrom rlang .data
-#' @import ggplot2
-#' @import dplyr
-#'
-#' @examples
-#' \dontrun{
-#' combine_GSEA_results <- function(gsea_results,
-#' pathways){
-#' gsea_results <- lapply(gsea_results, function(x){x %>% filter(pathway %in% pathways)})
-#' gsea_results <- data.table::rbindlist(gsea_results, idcol='ID')
-#' }
-#'
-#' pathways = c('REACTOME_SIGNALING_BY_GPCR', 'REACTOME_SIGNALING_BY_NTRKS')
-#' gsea_results <- list('FAC vs Cont' = gsea_result, 'LiproxposFAC vs Cont' = gsea_result_2)
-#' joint_GSEA_results <- combine_GSEA_results(gsea_results, pathways)
-#' gseaDotplot_joint(joint_GSEA_results)
-#' }
-gseaDotplot_joint <- function(gsea_results,
- pathway_order = NULL,
- x_order = NULL,
- significance = c(0.05, 0.01, 0.001),
- p_val_col = 'pval'){
- if (!is.null(pathway_order)) {
- if (all(pathway_order %in% unique(gsea_results$pathway))){
- pathway_order <- order(factor(gsea_results$pathway, levels = pathway_order))
- gsea_results$pathway <- .wrap_underscore_strings_balance(gsea_results$pathway,36)
- ## reordering
- gsea_results <- gsea_results[pathway_order,]
- gsea_results$pathway <- factor(gsea_results$pathway, levels = unique(gsea_results$pathway))
- } else {
- warning('pathways specified in pathway_order not found, defaulting to arbitrary order')
- }
- } else {
- gsea_results$pathway <- .wrap_underscore_strings_balance(gsea_results$pathway,36)
- }
-
- if (!is.null(x_order)) {
- if (all(x_order %in% unique(gsea_results$ID))){
- gsea_results$ID <- factor(gsea_results$ID, levels = x_order)
- } else {
- warning('Specified x_order not all found in data, defaulting to arbitrary order')
- }
- }
-
- gsea_results$label <- NA
- caption <- ''
- if (!is.null(significance)) {
- if (is.numeric(significance)) {
- label <- '*'
- for (cutoff in significance) {
- gsea_results$label <- ifelse(gsea_results[[p_val_col]] < cutoff, label, gsea_results$label)
- caption <- paste(caption, label, '<', cutoff, ';', sep = ' ')
- label <- paste0(label, '*')
- }
- # gsea_results$label[is.numeric(gsea_results$label)] <- NA
- } else {
- stop('Significance argument should be a numeric vector')
- }
- }
- ggplot(gsea_results, aes(x=.data$ID, y=.data$pathway, size=-log(.data[[p_val_col]]),
- color=.data$NES, label = .data$label)) +
- geom_point() +
- scale_color_gradient2(low="blue",
- mid="white",
- high="red",
- midpoint=0,
- breaks=c(-2,-1,0,1,2),
- limits=c(min(gsea_results$NES,-1),
- max(gsea_results$NES,1))) +
- theme_classic(11) +
- theme(panel.grid.major = element_line(colour = "grey92"),
- panel.grid.minor = element_line(colour = "grey92"),
- panel.grid.major.y = element_line(colour = "grey92"),#element_blank(),
- panel.grid.minor.y = element_line(colour = "grey92")) +
- theme(axis.text.x = element_text(angle = 90,
- vjust = 0.5,
- hjust=1)) +
- labs(x="Comparison",
- y="Gene set",
- color = "Normalized\nenrichment\nscore",
- size="Nom p-val",
- title="GSEA pathway enrichments",
- caption = caption) +
- scale_radius(name="NOM p-val",
- range=c(1,8),
- breaks=-log10(c(0.1,0.01,0.001,0.0001)),
- labels=c(0.1,0.01,0.001,0.0001)) +
- geom_text(na.rm = TRUE, color = 'white', size = 3)
-}
\ No newline at end of file
diff --git a/R/gseaDotplot_single.R b/R/gseaDotplot_single.R
deleted file mode 100644
index 0fcae4c..0000000
--- a/R/gseaDotplot_single.R
+++ /dev/null
@@ -1,121 +0,0 @@
-#' GSEA dotplot
-#'
-#' Make dotplot from fGSEA result, showing top n pathways
-#'
-#' @rdname gseaDotplot_single
-#' @param result A table with GSEA results from `fgsea::fgseaSimple()`
-#' @param min_size Minimum size of gene set to plot
-#' @param filter_source Character vector of pathway sources to filter for
-#' @param signif_only If TRUE, only plot results with p value < `sig_cutoff`
-#' @param top_n Show the top N results sorted by pval
-#' @param sig_cutoff Threshold for significance, default to 0.05
-#' @param significance A vector of values to indicate significance with asterisks.
-#' Each subsequent value will add an extra asterisk. E.g. `c(0.05, 0.01)` will
-#' give one asteriks to values below 0.05 and two asterisks to values below 0.01.
-#' If this is null, no asterisks will be plotted.
-#' @param use_shortened_pathway_names Pull names from column 'pathway_short'
-#' rather than pathway (if `runfgsea()` call had `breakdown_pathway_names` set
-#' to `TRUE`)
-#' @param p_val_col Column to use for significance values. Default 'pval'.
-#'
-#' @return A ggplot object
-#' @export
-#'
-#' @importFrom rlang .data
-#' @importFrom utils head
-#' @import ggplot2
-#' @import dplyr
-#'
-#' @examples
-#' \dontrun{
-#' res <- runfgsea(result, gmt.file)
-#' gseaDotplot(res, filter_source = "HALLMARK")
-#' }
-gseaDotplot_single <- function(result,
- filter_source = NULL,
- signif_only = FALSE,
- top_n = 20,
- min_size = 5,
- sig_cutoff = 0.05,
- use_shortened_pathway_names = FALSE,
- significance = c(0.05, 0.01, 0.001),
- p_val_col = 'pval') {
- if (use_shortened_pathway_names){
- result$pathway <- result$pathway_short
- }
- result <- result %>%
- arrange(.data[[p_val_col]], desc(.data$size)) %>%
- mutate(perc = 100 * lengths(.data$leadingEdge) / .data$size) %>%
- mutate(name = paste0(.wrap_underscore_strings_balance(.data$pathway, 36), "\nn=", .data$size)) %>%
- filter(.data$size >= min_size)
- if (!is.null(filter_source)) {
- result <- result %>%
- filter(.data$source %in% filter_source)
- }
- if (signif_only) {
- result <- result %>%
- filter(.data[[p_val_col]] < sig_cutoff)
- }
-
- result$label <- NA
- caption <- ''
- if (!is.null(significance)) {
- if (is.numeric(significance)) {
- label <- '*'
- for (cutoff in significance) {
- result$label <- ifelse(result$pval < cutoff, label, result$label)
- caption <- paste(caption, label, '<', cutoff, ';', sep = ' ')
- label <- paste0(label, '*')
- }
- # gsea_results$label[is.numeric(gsea_results$label)] <- NA
- } else {
- stop('Significance argument should be a numeric vector')
- }
- }
-
-
- toppaths <- rbind(utils::head(result, n = top_n))
- toppaths$name <- factor(toppaths$name)
- dotplot <- ggplot(toppaths,
- aes(
- x = .data[['perc']],
- y = .data[['name']],
- size = -log10(.data[['pval']]),
- color = .data[['NES']],
- label = .data[['label']])) +
- geom_point() +
- scale_color_gradient2(
- low = "blue",
- mid = "white",
- high = "red",
- midpoint = 0,
- breaks = c(-2, -1, 0, 1, 2),
- limits = c(
- min(toppaths$NES, -1),
- max(toppaths$NES, 1)
- )
- ) +
- theme_classic(11) +
- theme(
- panel.grid.major = element_line(colour = "grey92"),
- panel.grid.minor = element_line(colour = "grey92"),
- panel.grid.major.y = element_line(colour = "grey92"),
- panel.grid.minor.y = element_line(colour = "grey92")
- ) +
- theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +
- labs(
- x = "% of genes in leading edge", y = "Gene set",
- color = "Normalized\nenrichment\nscore",
- size = "Nom p-val", title = "Top enriched pathways",
- caption = paste0("n = number of genes in pathway\n", caption)) +
- scale_radius(
- name = "NOM p-val",
- range = c(1, 8),
- breaks = -log10(c(0.5, 0.1, 0.01, 0.001)),
- limits = c(0, 3),
- labels = c(0.5, 0.1, 0.01, 0.001)
- ) +
- scale_y_discrete(limits = toppaths$name) +
- geom_text(na.rm = TRUE, color = 'black', size = 3)
- return(dotplot)
-}
diff --git a/R/heatmapFromGenelist.R b/R/heatmapFromGenelist.R
index 67d5782..23da82f 100644
--- a/R/heatmapFromGenelist.R
+++ b/R/heatmapFromGenelist.R
@@ -45,20 +45,15 @@
#' ## Simple call
#' heatmapFromGenelist(
#' geneList = c("Ccl2", "Cxcl1", "Cxcl2", "Postn", "Fn1", "Thbs1"),
-#' data_to_plot,
-#' baseline_grouping = "Group",
-#' baseline = "Cont"
+#' data_to_plot
#' )
#'
-#' ## run with custom reordering of data and labeled slices
+#' ## run with labeled slices
#' heatmapFromGenelist(
#' geneList = c("Ccl2", "Cxcl1", "Cxcl2", "Postn", "Fn1", "Thbs1"),
#' data_to_plot,
-#' baseline_grouping = "Group",
-#' baseline = "Cont",
#' column_split = c(rep(1, 3), rep(2, 3), rep(3, 3), rep(4, 3)),
-#' slice_labels = c("Cont", "Fac", "L", "M"),
-#' data = assays(analysis$dds)$rld[, sort(colnames(assays(analysis$dds)$rld))]
+#' slice_labels = c("Cont", "Fac", "L", "M")
#' )
#' }
#'
diff --git a/R/utils.R b/R/utils.R
index ec7a969..26b26eb 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -21,3 +21,32 @@
string
}, character(1), width, indent, exdent, USE.NAMES = USE.NAMES)
}
+
+
+#' Read an excel workbook with sheets to a list of tables
+#'
+#' Read an excel workbook with sheets to a list of tables
+#'
+#' @param filename File in format .xls or .xlsx
+#' @param tibble BOOL, Return the data as a tibble instead of a data.frame
+#' @param \dots Additional arguments passed to `openxlsx::read.xlsx()`
+#'
+#' @returns A list of data.frames (or tibbles)
+#'
+#' @import openxlsx
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' dge_results <- read_excel_allsheets(here('outputs/dge.xlsx'))
+#' }
+read_excel_allsheets <- function(filename,
+ tibble = FALSE,
+ ...) {
+ # https://stackoverflow.com/a/12945838/15664425
+ sheets <- openxlsx::getSheetNames(filename)
+ x <- lapply(sheets, function(X) openxlsx::read.xlsx(filename, sheet = X, ...))
+ if(!tibble) x <- lapply(x, as.data.frame)
+ names(x) <- sheets
+ x
+}
\ No newline at end of file
diff --git a/man/gseaDotplot_joint.Rd b/man/gseaDotplot_joint.Rd
index 3d95732..0f2ad13 100644
--- a/man/gseaDotplot_joint.Rd
+++ b/man/gseaDotplot_joint.Rd
@@ -1,14 +1,17 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gseaDotplot_joint.R
+% Please edit documentation in R/gseaDotplot.R
\name{gseaDotplot_joint}
\alias{gseaDotplot_joint}
-\title{GSEA dotplot}
+\title{GSEA dotplot for multiple contrasts}
\usage{
gseaDotplot_joint(
gsea_results,
pathway_order = NULL,
x_order = NULL,
significance = c(0.05, 0.01, 0.001),
+ range = c(1, 8),
+ breaks = -log10(c(0.1, 0.01, 0.001, 1e-04)),
+ labels = c(0.1, 0.01, 0.001, 1e-04),
p_val_col = "pval"
)
}
@@ -25,6 +28,32 @@ Each subsequent value will add an extra asterisk. E.g. \code{c(0.05, 0.01)} will
give one asteriks to values below 0.05 and two asterisks to values below 0.01.
If this is null, no asterisks will be plotted.}
+\item{range}{a numeric vector of length 2 that specifies the minimum and
+maximum size of the plotting symbol after transformation.}
+
+\item{breaks}{One of:
+\itemize{
+\item \code{NULL} for no breaks
+\item \code{waiver()} for the default breaks computed by the
+\link[scales:trans_new]{transformation object}
+\item A numeric vector of positions
+\item A function that takes the limits as input and returns breaks
+as output (e.g., a function returned by \code{\link[scales:breaks_extended]{scales::extended_breaks()}}).
+Also accepts rlang \link[rlang:as_function]{lambda} function notation.
+}}
+
+\item{labels}{One of:
+\itemize{
+\item \code{NULL} for no labels
+\item \code{waiver()} for the default labels computed by the
+transformation object
+\item A character vector giving labels (must be same length as \code{breaks})
+\item An expression vector (must be the same length as breaks). See ?plotmath for details.
+\item A function that takes the breaks as input and returns labels
+as output. Also accepts rlang \link[rlang:as_function]{lambda} function
+notation.
+}}
+
\item{p_val_col}{Column to use for significance values. Default 'pval'.}
}
\value{
diff --git a/man/gseaDotplot_single.Rd b/man/gseaDotplot_single.Rd
index b3ebc22..6d83006 100644
--- a/man/gseaDotplot_single.Rd
+++ b/man/gseaDotplot_single.Rd
@@ -1,8 +1,8 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gseaDotplot_single.R
+% Please edit documentation in R/gseaDotplot.R
\name{gseaDotplot_single}
\alias{gseaDotplot_single}
-\title{GSEA dotplot}
+\title{GSEA dotplot for a single contrast}
\usage{
gseaDotplot_single(
result,
@@ -13,6 +13,9 @@ gseaDotplot_single(
sig_cutoff = 0.05,
use_shortened_pathway_names = FALSE,
significance = c(0.05, 0.01, 0.001),
+ range = c(1, 8),
+ breaks = -log10(c(0.1, 0.01, 0.001, 1e-04)),
+ labels = c(0.1, 0.01, 0.001, 1e-04),
p_val_col = "pval"
)
}
@@ -38,13 +41,39 @@ Each subsequent value will add an extra asterisk. E.g. \code{c(0.05, 0.01)} will
give one asteriks to values below 0.05 and two asterisks to values below 0.01.
If this is null, no asterisks will be plotted.}
+\item{range}{a numeric vector of length 2 that specifies the minimum and
+maximum size of the plotting symbol after transformation.}
+
+\item{breaks}{One of:
+\itemize{
+\item \code{NULL} for no breaks
+\item \code{waiver()} for the default breaks computed by the
+\link[scales:trans_new]{transformation object}
+\item A numeric vector of positions
+\item A function that takes the limits as input and returns breaks
+as output (e.g., a function returned by \code{\link[scales:breaks_extended]{scales::extended_breaks()}}).
+Also accepts rlang \link[rlang:as_function]{lambda} function notation.
+}}
+
+\item{labels}{One of:
+\itemize{
+\item \code{NULL} for no labels
+\item \code{waiver()} for the default labels computed by the
+transformation object
+\item A character vector giving labels (must be same length as \code{breaks})
+\item An expression vector (must be the same length as breaks). See ?plotmath for details.
+\item A function that takes the breaks as input and returns labels
+as output. Also accepts rlang \link[rlang:as_function]{lambda} function
+notation.
+}}
+
\item{p_val_col}{Column to use for significance values. Default 'pval'.}
}
\value{
A ggplot object
}
\description{
-Make dotplot from fGSEA result, showing top n pathways
+Make dotplot from an fGSEA result, showing top n pathways
}
\examples{
\dontrun{
diff --git a/man/heatmapFromGenelist.Rd b/man/heatmapFromGenelist.Rd
index 61062d4..2c907d5 100644
--- a/man/heatmapFromGenelist.Rd
+++ b/man/heatmapFromGenelist.Rd
@@ -172,20 +172,15 @@ data_to_plot <- normalizeCountsForHeatmapByIndividual(assay(assays(obj.pbmc)$rld
## Simple call
heatmapFromGenelist(
geneList = c("Ccl2", "Cxcl1", "Cxcl2", "Postn", "Fn1", "Thbs1"),
- data_to_plot,
- baseline_grouping = "Group",
- baseline = "Cont"
+ data_to_plot
)
-## run with custom reordering of data and labeled slices
+## run with labeled slices
heatmapFromGenelist(
geneList = c("Ccl2", "Cxcl1", "Cxcl2", "Postn", "Fn1", "Thbs1"),
data_to_plot,
- baseline_grouping = "Group",
- baseline = "Cont",
column_split = c(rep(1, 3), rep(2, 3), rep(3, 3), rep(4, 3)),
- slice_labels = c("Cont", "Fac", "L", "M"),
- data = assays(analysis$dds)$rld[, sort(colnames(assays(analysis$dds)$rld))]
+ slice_labels = c("Cont", "Fac", "L", "M")
)
}
diff --git a/man/read_excel_allsheets.Rd b/man/read_excel_allsheets.Rd
new file mode 100644
index 0000000..a0e582c
--- /dev/null
+++ b/man/read_excel_allsheets.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{read_excel_allsheets}
+\alias{read_excel_allsheets}
+\title{Read an excel workbook with sheets to a list of tables}
+\usage{
+read_excel_allsheets(filename, tibble = FALSE, ...)
+}
+\arguments{
+\item{filename}{File in format .xls or .xlsx}
+
+\item{tibble}{BOOL, Return the data as a tibble instead of a data.frame}
+
+\item{\dots}{Additional arguments passed to \code{openxlsx::read.xlsx()}}
+}
+\value{
+A list of data.frames (or tibbles)
+}
+\description{
+Read an excel workbook with sheets to a list of tables
+}
+\examples{
+\dontrun{
+ dge_results <- read_excel_allsheets(here('outputs/dge.xlsx'))
+}
+}