Visualisation of distributions using ggplot2-based boxplots.
vis_box(.data, .by = NA, .meta = NA, .melt = T, .points = T, .test = T, .signif.label.size = 3.5, .defgroupby = "Sample", .grouping.var = "Group", .labs = c("X", "Y"), .title = "Boxplot (.title argument)", .subtitle = "Subtitle (.subtitle argument)", .legend = NA, .leg.title = "Legend (.leg.title argument)")
.data | Input matrix or data frame. |
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.by | Pass NA if you want to plot samples without grouping. You can pass a character vector with one or several column names from ".meta" to group your data before plotting. In this case you should provide ".meta". You can pass a character vector that exactly matches the number of samples in your data, each value should correspond to a sample's property. It will be used to group data based on the values provided. Note that in this case you should pass NA to ".meta". |
.meta | A metadata object. An R dataframe with sample names and their properties, such as age, serostatus or hla. |
.melt | If TRUE then apply melt to the ".data" before plotting. In this case ".data" is supposed to be a data frame with the first character column reserved for names of genes and other numeric columns reserved to counts or frequencies of genes. Each numeric column should be associated with a specific repertoire sample. |
.points | A logical value defining whether points will be visualised or not. |
.test | A logical vector whether statistical tests should be applied. See "Details" for more information. |
.signif.label.size | An integer value defining the size of text for p-value. |
.defgroupby | A name for the column with sample names. |
.grouping.var | A name for the column to group by. |
.labs | Character vector of length two with names for x-axis and y-axis, respectively. |
.title | The text for the title of the plot. |
.subtitle | The The text for the plot's subtitle. |
.legend | If TRUE then displays a legend, otherwise removes legend from the plot. |
.leg.title | The The text for the plots's legend. Provide NULL to remove the legend's title completely. |