Description Usage Arguments Value Examples
Make MA-plot which is a scatter plot of log2 fold changes (on the y-axis) versus the mean expression signal (on the x-axis).
1 2 3 4 5 6 | ggmaplot(data, fdr = 0.05, fc = 1.5, genenames = NULL,
detection_call = NULL, size = NULL, font.label = c(12, "plain",
"black"), label.rectangle = FALSE, palette = c("#B31B21", "#1465AC",
"darkgray"), top = 15, select.top.method = c("padj", "fc"), main = NULL,
xlab = "Log2 mean expression", ylab = "Log2 fold change",
ggtheme = theme_classic(), ...)
|
data |
an object of class DESeqResults, get_diff, DE_Results, matrix or data frame containing the columns baseMean, log2FoldChange, and padj. Rows are genes.
|
fdr |
Accepted false discovery rate for considering genes as differentially expressed. |
fc |
the fold change threshold. Only genes with a fold change >= fc and padj <= fdr are considered as significantly differentially expressed. |
genenames |
a character vector of length nrow(data) specifying gene names corresponding to each row. Used for point labels. |
detection_call |
a numeric vector with length = nrow(data), specifying if the genes is expressed (value = 1) or not (value = 0). For example detection_call = c(1, 1, 0, 1, 0, 1). Default is NULL. If detection_call column is available in data, it will be used. |
size |
points size. |
font.label |
a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of point labels. For example font.label = c(14, "bold", "red"). |
label.rectangle |
logical value. If TRUE, add rectangle underneath the text, making it easier to read. |
palette |
the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty". |
top |
the number of top genes to be shown on the plot. Use top = 0 to hide to gene labels. |
select.top.method |
methods to be used for selecting top genes. Allowed values include "padj" and "fc" for selecting by adjusted p values or fold changes, respectively. |
main |
plot main title. |
xlab |
character vector specifying x axis labels. Use xlab = FALSE to hide xlab. |
ylab |
character vector specifying y axis labels. Use ylab = FALSE to hide ylab. |
ggtheme |
function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), .... |
... |
other arguments to be passed to |
returns a ggplot.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | data(diff_express)
# Default plot
ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"),
fdr = 0.05, fc = 2, size = 0.4,
palette = c("#B31B21", "#1465AC", "darkgray"),
genenames = as.vector(diff_express$name),
legend = "top", top = 20,
font.label = c("bold", 11),
font.legend = "bold",
font.main = "bold",
ggtheme = ggplot2::theme_minimal())
# Add rectangle around labels
ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"),
fdr = 0.05, fc = 2, size = 0.4,
palette = c("#B31B21", "#1465AC", "darkgray"),
genenames = as.vector(diff_express$name),
legend = "top", top = 20,
font.label = c("bold", 11), label.rectangle = TRUE,
font.legend = "bold",
font.main = "bold",
ggtheme = ggplot2::theme_minimal())
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