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Bubble plot showing the signature scores by self-defined groups

draw_bubbleplot.Rd

This function is used to draw a bubble plot of signature scores among self-defined groups.

Usage

draw_bubbleplot(
  input_eset,
  signature_table = NULL,
  group_by = "clusterID",
  colors = NULL,
  legend.position = "right",
  fontsize.legend_title = 10,
  fontsize.legend_text = 8,
  fontsize.axis_title = 10,
  fontsize.axis_text = 8,
  xlabel.angle = 0
)

Arguments

input_eset

The expression set object that filtered, normalized and log-transformed

signature_table

A matrix or data frame containing three columns: signature_name, signature_feature, weight. Default: NULL.

group_by

Character, name of the column for grouping, usually the column of cell types or clusters. Default: "clusterID".

colors

A vector of two colors indicating the low and high values respectively. Default: c("lightgrey", "red").

legend.position

Character, position of legend: "right" (the default), "left", "top", "bottom" or "none".

fontsize.legend_title

Integer, font size of the legend title. Default: 10.

fontsize.legend_text

Integer, font size of the legend text. Default: 8.

fontsize.axis_title

Integer, font size of the axis label and text. Default: 10.

fontsize.axis_text

Integer, font size of the axis label and text. Default: 8.

xlabel.angle

Numeric, the angle of the a-axis title. When it's set not 0, the x-axis text will automatically right-justified. Default: 0.

Value

A ggplot object of bubble plot

Examples

data(pbmc14k_expression.eset)
signature_table <- read.table(system.file('extdata/demo_pbmc14k/PBMC14k_signatureTable.txt', package = "scMINER"), header = TRUE, sep = "\t", quote = "", stringsAsFactors = FALSE)
head(signature_table)
#>   signature_name signature_feature weight
#> 1       Monocyte              CD14      1
#> 2       Monocyte               LYZ      1
#> 3       Monocyte            S100A8      1
#> 4       Monocyte            S100A9      1
#> 5       Monocyte           S100A12      1
#> 6             NK            FCGR3A      1

## 1. the most commonly used command
draw_bubbleplot(input_eset = pbmc14k_expression.eset,
                signature_table = signature_table,
                group_by = "clusterID")
#> 31 features of 7 signatures were found in the input eset and will be used in calculation.


## 2. customize the colors
draw_bubbleplot(input_eset = pbmc14k_expression.eset,
                signature_table = signature_table,
                group_by = "clusterID",
                colors = c("lightgrey", "red"))
#> 31 features of 7 signatures were found in the input eset and will be used in calculation.