This function subsets the numeric columns from the input data and compares them based on a selected grouping column. It computes the fold changes (ratio of means) and associated p-values (using two-sample t-tests) for each numeric variable between two groups. The results are log2-transformed (for fold change) and -log10-transformed (for p-values) to generate volcano plots.
Usage
cyt_volc(
data,
group_col,
cond1 = NULL,
cond2 = NULL,
fold_change_thresh = 2,
p_value_thresh = 0.05,
top_labels = 10,
output_file = NULL,
progress = NULL
)Arguments
- data
A matrix or data frame containing the data to be analyzed.
- group_col
A character string specifying the column name used for comparisons.
- cond1
A character string specifying the name of the first condition for comparison. If empty, all pairwise comparisons will be generated.
- cond2
A character string specifying the name of the second condition for comparison. If empty, all pairwise comparisons will be generated.
- fold_change_thresh
A numeric threshold for the fold change. Default is 2.
- p_value_thresh
A numeric threshold for the p-value. Default is 0.05.
- top_labels
An integer specifying the number of top variables to label on the plot. Default is 10.
- output_file
Optional. A file path to save the plot. If NULL (default), the function returns a list of ggplot objects.
Value
If output_file is NULL, a list of ggplot objects (one per pair) is returned. If output_file is provided, the plot(s) are written to that file and the function returns NULL invisibly.
Details
If both cond1 and cond2 are provided (non-empty), only that pair is compared. Otherwise, the function automatically generates all possible pairwise comparisons.
Examples
# Loading data
data_df <- ExampleData1[,-c(2:3)]
cyt_volc(data_df, "Group", cond1 = "T2D", cond2 = "ND",
fold_change_thresh = 2.0, top_labels= 15)
#> $plot
#>
#> $stats
#> variable fc_log p_log significant
#> IL.12.P70 IL.12.P70 -2.60117683 2.18641971 TRUE
#> IL.6 IL.6 -0.95013174 3.94758527 FALSE
#> IL.27 IL.27 -0.67878724 2.33099419 FALSE
#> IL.23 IL.23 -0.87320747 1.95290632 FALSE
#> CCL.20.MIP.3A CCL.20.MIP.3A -0.48569948 1.40917287 FALSE
#> IL.2 IL.2 -0.80577278 1.22848122 FALSE
#> IL.17F IL.17F -0.93024059 1.16938373 FALSE
#> IL.10 IL.10 -0.48121242 1.01734902 FALSE
#> IL.28A IL.28A -0.31081278 0.98351262 FALSE
#> IL.17A IL.17A -0.80415853 0.90173665 FALSE
#> IL.1B IL.1B -0.61564856 0.83381951 FALSE
#> GM.CSF GM.CSF 0.45980342 0.62042612 FALSE
#> IL.21 IL.21 -0.62254771 0.51843946 FALSE
#> IL.17E.IL.25 IL.17E.IL.25 0.01449957 0.49515782 FALSE
#> IL.22 IL.22 -0.30363695 0.47550506 FALSE
#> IL.9 IL.9 -0.32752255 0.43117675 FALSE
#> TNF.A TNF.A -0.15647551 0.21142412 FALSE
#> IL.31 IL.31 0.21056699 0.20929529 FALSE
#> IL.4 IL.4 0.21161574 0.20542291 FALSE
#> IL.5 IL.5 -0.20808037 0.17512546 FALSE
#> IL.15 IL.15 -0.05298748 0.12055764 FALSE
#> IL.13 IL.13 -0.07717527 0.06654004 FALSE
#> IFN.G IFN.G -0.09088794 0.06221451 FALSE
#> TNF.B TNF.B 0.07037796 0.05224667 FALSE
#> IL.33 IL.33 0.01213249 0.01719622 FALSE
#>