dot_plot | R Documentation |
Function to cutomise the Dot Plot of CellPhoneDB analysis results.
dot_plot( vgm.input, selected.rows, selected.columns, threshold.type, threshold.value, project.name, filename, width, height, text.size, return.vector, platypus.version )
vgm.input |
Output of the VDJ_GEX_matrix function. Mandatory. Object where to save the dotplot. |
selected.rows |
Strings vector. Defaults to NULL. Vector of rows to plot (interacting genes pair), one per line. |
selected.columns |
Strings vector. Defaults to NULL. Vector of columns (interacting groups) to plot, one per line |
threshold.type |
Character vector. Defaults to NULL. Possible arguments: "pvalue", "log2means", "pvalue_topn", "log2means_topn". Which thresholding system the user wants to use. |
threshold.value |
Numerical. Defaults to NULL. Value below/above (depending on whether it's pvalue or log2means) which genes to plot are selected. |
project.name |
Character vector. Defaults to NULL. Subfolder where to find the output of the CellPhoneDB analysis and where to save the dot_plot output plot. |
filename |
Character vector. Defaults to "selection_plot.pdf". Name of the file where the dot_plot output plot will be saved. |
width |
Numerical. Defaults to 8. Width of the plot. |
height |
Numerical. Defaults to 10. Height of the plot. |
text.size |
Numerical. Defaults to 12. Font size of the plot axes |
return.vector |
Logical. Defaults to FALSE. If set to TRUE, it includes the vector of genes_pairs present in the dot_plot in the VDJ_GEX_matrix[[10]] list. |
platypus.version |
This function works with "v3" only, there is no need to set this parameter |
VDJ_GEX_matrix object with output dot plot added to VDJ_GEX_matrix[[10]] list.
## Not run: vgm_cellphonedb<-dot_plot(vgm.input=vgm_cellphonedb, selected.columns = c("group_1_3|group_2_6", "group_1_3|group_3_9", "group_2_6|group_1_3", "group_2_6|group_3_9", "group_3_9|group_1_3", "group_3_9|group_2_6"), threshold.type="pvalue_topn", threshold.value=50, project.name = "test", height = 12, width=6, text.size=10, return.vector=TRUE) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.