doc_function: Mock function used to document all main function.

In SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

Mock function used to document all main function.

Description

Mock function used to document all main function.

Arguments

sample	Seurat | A Seurat object, generated by CreateSeuratObject.
font.size	numeric | Overall font size of the plot. All plot elements will have a size relationship with this font size.
font.type	character | Base font family for the plot. One of: mono: Mono spaced font. serif: Serif font family. sans: Default font family.
legend.type	character | Type of legend to display. One of: normal: Default legend displayed by ggplot2. colorbar: Redefined colorbar legend, using guide_colorbar.
legend.position	character | Position of the legend in the plot. One of: top: Top of the figure. bottom: Bottom of the figure. left: Left of the figure. right: Right of the figure. none: No legend is displayed.
legend.framewidth, legend.tickwidth	numeric | Width of the lines of the box in the legend.
legend.framecolor	character | Color of the lines of the box in the legend.
legend.tickcolor	character | Color of the ticks of the box in the legend.
legend.length, legend.width	numeric | Length and width of the legend. Will adjust automatically depending on legend side.
plot.title, plot.subtitle, plot.caption	character | Title, subtitle or caption to use in the plot.
assay	character | Assay to use. Defaults to the current assay.
slot	character | Data slot to use. Only one of: counts, data, scale.data. Defaults to "data".
reduction	character | Reduction to use. Can be the canonical ones such as "umap", "pca", or any custom ones, such as "diffusion". If you are unsure about which reductions you have, use Seurat::Reductions(sample). Defaults to "umap" if present or to the last computed reduction if the argument is not provided.
viridis.palette	character | A capital letter from A to H or the scale name as in scale_fill_viridis.
raster	logical | Whether to raster the resulting plot. This is recommendable if plotting a lot of cells.
raster.dpi	numeric | Pixel resolution for rasterized plots. Defaults to 1024. Only activates on Seurat versions higher or equal than 4.1.0.
plot_cell_borders	logical | Whether to plot border around cells.
border.size	numeric | Width of the border of the cells.
border.color	character | Color for the border of the heatmap body.
na.value	character | Color value for NA.
axis.text.x.angle	numeric | Degree to rotate the X labels. One of: 0, 45, 90.
xlab, ylab	character | Titles for the X and Y axis.
pt.size	numeric | Size of the dots.
verbose	logical | Whether to show extra comments, warnings,etc.
flip	logical | Whether to invert the axis of the displayed plot.
group.by	character | Metadata variable to group the output by. Has to be a character of factor column.
split.by	character | Secondary metadata variable to further group (split) the output by. Has to be a character of factor column.
colors.use	named_vector | Named vector of valid color representations (either name of HEX codes) with as many named colors as unique values of group.by. If group.by is not provided, defaults to the unique values of Idents. If not provided, a color scale will be set by default.
legend.title	character | Title for the legend.
legend.icon.size	numeric | Size of the icons in legend.
legend.byrow	logical | Whether the legend is filled by row or not.
legend.ncol	numeric | Number of columns in the legend.
legend.nrow	numeric | Number of rows in the legend.
plot_marginal_distributions	logical | Whether to plot marginal distributions on the figure or not.
marginal.type	character | One of: density: Compute density plots on the margins. histogram: Compute histograms on the margins. boxplot: Compute boxplot on the margins. violin: Compute violin plots on the margins. densigram: Compute densigram plots on the margins.
marginal.size	numeric | Size ratio between the main and marginal plots. A value of 5 means that the main plot is 5 times bigger than the marginal plots.
marginal.group	logical | Whether to group the marginal distribution by group.by or current identities.
enforce_symmetry	logical | Return a symmetrical plot axes-wise or continuous color scale-wise, when applicable.
column_title	character | Title for the columns of the heatmaps. Only works with single heatmaps.
row_title	character | Title for the rows of the heatmaps. Only works with single heatmaps.
cluster_cols	logical | Cluster the columns or rows of the heatmaps.
cluster_rows	logical | Cluster the rows or rows of the heatmaps.
column_names_rot	numeric | Degree in which to rotate the column labels.
row_names_rot	numeric | Degree in which to rotate the row labels.
cell_size	numeric | Size of each cell in the heatmap.
input_gene_list	named_list | Named list of lists of genes to be used as input.
column_title_rot	numeric | Degree in which to rotate the column titles.
row_title_rot	numeric | Degree in which to rotate the row titles.
column_names_side	character | Side to put the column names. Either left or right.
row_names_side	character | Side to put the row names. Either left or right.
column_title_side	character | Side to put the column titles Either left or right.
row_title_side	character | Side to put the row titles Either left or right.
heatmap.legend.length, heatmap.legend.width	numeric | Width and length of the legend in the heatmap.
heatmap.legend.framecolor	character | Color of the edges and ticks of the legend in the heatmap.
scale_direction	numeric | Direction of the viridis scales. Either -1 or 1.
heatmap_gap	numeric | Gap in cm between heatmaps.
legend_gap	numeric | Gap in cm between legends.
cells.highlight, idents.highlight	character | Vector of cells/identities to focus into. The identities have to much those in Seurat::Idents(sample) The rest of the cells will be grayed out. Both parameters can be used at the same time.
ncol	numeric | Number of columns used in the arrangement of the output plot using "split.by" parameter.
dims	numeric | Vector of 2 numerics indicating the dimensions to plot out of the selected reduction. Defaults to c(1, 2) if not specified.
feature	character | Feature to represent.
features	character | Features to represent.
use_viridis	logical | Whether to use viridis color scales.
viridis.direction	numeric | Either 1 or -1. Controls how the gradient of viridis scale is formed.
plot.grid	logical | Whether to plot grid lines.
grid.color	character | Color of the grid in the plot. In heatmaps, color of the border of the cells.
grid.type	character | One of the possible linetype options: blank. solid. dashed. dotted. dotdash. longdash. twodash.
plot.axes	logical | Whether to plot axes or not.
individual.titles, individual.subtitles, individual.captions	character | Vector. Title, subtitle or caption to use in the plot when multiple features are passed on. Use NA to keep the original title.
legend.title.position	character | Position for the title of the legend. One of: top: Top of the legend. bottom: Bottom of the legend. left: Left of the legend. right: Right of the legend.
repel	logical | Whether to repel the text labels.
plot_density_contour	logical | Whether to plot density contours in the UMAP.
contour.position	character | Whether to plot density contours on top or at the bottom of the visualization layers, thus overlapping the clusters/cells or not.
contour.color	character | Color of the density lines.
contour.lineend	character | Line end style (round, butt, square).
contour.linejoin	character | Line join style (round, mitre, bevel).
contour_expand_axes	numeric | To make the contours fit the plot, the limits of the X and Y axis are expanding a given percentage from the min and max values for each axis. This controls such percentage.
label	logical | Whether to plot the cluster labels in the UMAP. The cluster labels will have the same color as the cluster colors.
label.color	character | Color of the labels in the plot.
label.fill	character | Color to fill the labels. Has to be a single color, that will be used for all labels. If NULL, the colors of the clusters will be used instead.
label.size	numeric | Size of the labels in the plot.
label.box	logical | Whether to plot the plot labels as geom_text (FALSE) or geom_label (TRUE).
min.overlap	numeric | Filter the output result to the terms which are supported by this many genes.
GO_ontology	character | GO ontology to use. One of: BP: For Biological Process. MF: For Molecular Function. CC: For Cellular Component.
genes	character | Vector of gene symbols to query for functional annotation.
org.db	OrgDB | Database object to use for the query.
disable_white_in_viridis	logical | Remove the white in viridis color scale when viridis.direction is set to -1.
number.breaks	numeric | Controls the number of breaks in continuous color scales of ggplot2-based plots.
strip.spacing	numeric | Controls the size between the different facets.
strip.text.color	character | Color of the strip text.
strip.text.angle	numeric | Rotation of the strip text (angles).
diverging.palette	character | Type of symmetrical color palette to use. Out of the diverging palettes defined in brewer.pal.
diverging.direction	numeric | Either 1 or -1. Direction of the divering palette. This basically flips the two ends.
subsample	numeric | Number of cells to subset for the analysis. NA will use all. Cells are selected at random.
plot.title.face, plot.subtitle.face, plot.caption.face, axis.title.face, axis.text.face, legend.title.face, legend.text.face	character | Controls the style of the font for the corresponding theme element. One of: plain: For normal text. italic: For text in itallic. bold: For text in bold. bold.italic: For text both in itallic and bold.
flavor	character | One of: Seurat, UCell. Compute the enrichment scores using AddModuleScore or AddModuleScore_UCell.
features.order	character | Should the gene sets be ordered in a specific way? Provide it as a vector of characters with the same names as the names of the gene sets.
groups.order	named_list | Should the groups in theheatmaps be ordered in a specific way? Provide it as a named list (as many lists as values in group.by) with the order for each of the elements in the groups.
interpolate	logical | Smoothes the output heatmap, saving space on disk when saving the image. However, the image is not as crisp.
viridis.palette.pvalue, viridis.palette.logfc, viridis.palette.expression	character | Viridis color palettes for the p-value, logfc and expression heatmaps. A capital letter from A to H or the scale name as in scale_fill_viridis.
nbin	numeric | Number of bins to use in AddModuleScore.
ctrl	numeric | Number of genes in the control set to use in AddModuleScore.
min.cutoff, max.cutoff	numeric | Set the min/max ends of the color scale. Any cell/group with a value lower than min.cutoff will turn into min.cutoff and any cell with a value higher than max.cutoff will turn into max.cutoff. In FeaturePlots, provide as many values as features. Use NAs to skip a feature.
border.density	numeric | Controls the number of cells used when plot_cell_borders = TRUE. Value between 0 and 1. It computes a 2D kernel density and based on this cells that have a density below the specified quantile will be used to generate the cluster contour. The lower this number, the less cells will be selected, thus reducing the overall size of the plot but also potentially preventing all the contours to be properly drawn.
sequential.palette	character | Type of sequential color palette to use. Out of the sequential palettes defined in brewer.pal.
sequential.palette.pvalue, sequential.palette.expression, sequential.palette.logfc	character | Sequential palettes for p-value, logfc and expression heatmaps. Type of sequential color palette to use. Out of the sequential palettes defined in brewer.pal.
sequential.direction	numeric | Direction of the sequential color scale. Either 1 or -1.
return_object	logical | Returns the Seurat object with the modifications performed in the function. Nomally, this contains a new assay with the data that can then be used for any other visualization desired.
statistic	character | DecoupleR statistic to use. One of: wmean: For weighted mean. norm_wmean: For normalized weighted mean. corr_wmean: For corrected weighted mean.
cluster	logical | Whether to perform clustering of rows and columns.

Value

Nothing. This is a mock function.

Examples

# This a mock function that stores the documentation for many other functions.
# It is not intended for user usage.

SCpubr documentation built on Oct. 11, 2023, 5:15 p.m.