Generates a heatmap of DEMs generated from edgeR analysis run using FindAllDEMs().
This function uses pheatmap to plot data.
Usage
DEMsHeatmap(
edgeR_output,
n = 5,
only.pos = FALSE,
FDR.threshold = 0.05,
logfc.threshold = 0.5,
order.by = "FDR",
scale = "row",
color = (grDevices::colorRampPalette(c("navy", "white", "red")))(50),
cluster_cols = FALSE,
cluster_rows = TRUE,
fontsize_row = 15,
fontsize_col = 15,
cutree_cols = 9,
silent = TRUE,
plot_annotations_column = NULL,
save_to_path = NULL,
plot.save.width = 20,
plot.save.height = 20,
nlabels.to.show = NULL,
annotation_colors = NULL
)Arguments
- edgeR_output
A list containing outputs from edgeR analysis (from FindAllDEMs()). This includes pseudo-bulked counts and DEMs.
- n
A numeric integer that defines the number of UP and DOWN regulated peaks to plot (default = 25).
- only.pos
Boolean indicating if only positive markers should be returned (default = FALSE).
- FDR.threshold
Numeric value that defines the FDR threshold to use for defining most significant results (default = 0.05).
- logfc.threshold
Numeric value that defines the logFC threshold to use for filtering significant results (default = 0.5).
- order.by
Character string defining which parameter to order markers by, options are either 'FDR' or 'logFC' (default = "FDR").
- scale
A character string indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none"
- color
A vector of colors used in heatmap (default = grDevices::colorRampPalette(c("navy", "white", "red"))(50)).
- cluster_cols
Boolean value determining if columns should be clustered or hclust object (default = FALSE).
- cluster_rows
Boolean value determining if rows should be clustered or hclust object (default = TRUE).
- fontsize_row
A numeric value defining the fontsize of rownames (default = 15).
- fontsize_col
A numeric value defining the fontsize of colnames (default = 15).
- cutree_cols
A numeric value defining the number of clusters the columns are divided into, based on the hierarchical clustering(using cutree), if cols are not clustered, the argument is ignored (default = 9).
- silent
Boolean value indicating if the plot should not be draw (default = TRUE).
- plot_annotations_column
Character string indicating the column name that contains the metabolite annotations to plot. Annotations = TRUE must be used in FindAllDEMs() for edgeR output to include annotations. If plot_annotations_column = NULL, m/z vaues will be plotted (default = NULL).
- save_to_path
Character string defining the full filepath and name of the plot to be saved as.
- plot.save.width
Integer value representing the width of the saved pdf plot (default = 20).
- plot.save.height
Integer value representing the height of the saved pdf plot (default = 20).
- nlabels.to.show
Numeric value defining the number of annotations to show per m/z (default = NULL).
- annotation_colors
List for specifying annotation_row and annotation_col track colors manually. Check pheatmap R-Package documentation for details. If set to 'NA', default coloring will be used (default = NA).
Value
A heatmap plot of significantly differentially expressed metabolites defined in the edgeR ouput object.
Examples
utils::str(formals(DEMsHeatmap))
#> Dotted pair list of 20
#> $ edgeR_output : symbol
#> $ n : num 5
#> $ only.pos : logi FALSE
#> $ FDR.threshold : num 0.05
#> $ logfc.threshold : num 0.5
#> $ order.by : chr "FDR"
#> $ scale : chr "row"
#> $ color : language (grDevices::colorRampPalette(c("navy", "white", "red")))(50)
#> $ cluster_cols : logi FALSE
#> $ cluster_rows : logi TRUE
#> $ fontsize_row : num 15
#> $ fontsize_col : num 15
#> $ cutree_cols : num 9
#> $ silent : logi TRUE
#> $ plot_annotations_column: NULL
#> $ save_to_path : NULL
#> $ plot.save.width : num 20
#> $ plot.save.height : num 20
#> $ nlabels.to.show : NULL
#> $ annotation_colors : NULL
# DEMs <- FindAllDEMs(SeuratObj, "sample")
# DEMsHeatmap(DEMs)