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Create an MD plot from expression data

Source: R/plot-md.R
plot_md.Rd

Create an MD (MA) plot from a data.frame containing differential expression results.

Usage

plot_md(
  df,
  x = "logCPM",
  y = "logFC",
  sig_col = "FDR",
  lab = NULL,
  fdr = 0.05,
  lfc = 0,
  annotate_counts = TRUE,
  label_sig = FALSE,
  up_color = "red2",
  down_color = "royalblue2",
  nonde_color = "grey40",
  up_alpha = 1,
  down_alpha = 1,
  nonde_alpha = 1,
  up_size = 1,
  down_size = 1,
  nonde_size = 1,
  up_shape = 16,
  down_shape = 16,
  nonde_shape = ".",
  xmax_label_offset = 0.85,
  ymax_label_offset = 0.8,
  ymin_label_offset = 0.8,
  lab_size = 6,
  lab_digits = 1,
  x_axis_limits = NULL,
  y_axis_limits = NULL,
  ...
)

Arguments

df

dataframe containing log-fold-change, p-value, and logCPM columns.

x

column in dataframe containing the logCPM data. Default ("logCPM")

y

column in dataframe containing the log-fold-change values. Default ("logFC")

sig_col

column in dataframe containing the results from significance testing. Default ("FDR")

lab

column in dataframe containing the labels to plot if label_sig = TRUE. Default NULL

fdr

numeric. Significance level cutoff for plotting. Values below the given fdr threshold are considered significant. Default (0.05)

lfc

numeric. Log-fold-change cutoff for plotting. Values greater than the abs(lfc) and less than fdr are displayed as differentially expressed. Default(0)

annotate_counts

TRUE/FALSE. Annotate the plot with the summarized gene counts

label_sig

logical. Apply ggrepel::geom_text_repel() to significant DE genes. Default FALSE

up_color

Point color of the up-regulated features. Default ("red2")

down_color

Point color of the down-regulated features. Default ("royalblue2")

nonde_color

Point color of the unperturbed features. Default ("grey40")

up_alpha

Point alpha value of the up-regulated features. Default (1)

down_alpha

Point alpha value of the down-regulated features. Default (1)

nonde_alpha

Point alpha value of the unperturbed features. Default (1)

up_size

Point size of the up-regulated features. Default (1)

down_size

Point size of the down-regulated features. Default (1)

nonde_size

Point size of the unperturbed features. Default (1)

up_shape

Point shape of the up-regulated features

down_shape

Point shape of the down-regulated features

nonde_shape

Point shape of the unperturbed features

xmax_label_offset

numeric. Value between 0 and 1 inclusive. Controls the x-position of the count labels

ymax_label_offset

numeric. Value between 0 and 1 inclusive. Controls the y-position of the 'up' count label

ymin_label_offset

numeric. Value between 0 and 1 inclusive. Controls the y-position of the 'down' count label

lab_size

numeric. If annotate_counts = TRUE specify the label size. Default = 6.

lab_digits

numeric. The number of digits used when rounding percentage values when annotate_counts=TRUE. Default (1)

x_axis_limits

numeric vector of axis limits supplied to ggplot2::coord_cartesian(). Default (NULL)

y_axis_limits

numeric vector of axis limits supplied to ggplot2::coord_cartesian(). Default (NULL)

...

Additional arguments passed to ggrepel::geom_text_repel()

Value

ggplot MD plot

Examples

plot_md(GSE161650_de, fdr = 0.01, lfc = log2(2))