fingerprintplot {BloodGen3Module} | R Documentation |
Individual fingerprint visualization The fingerprintplot function will generate fingerprint heatmap plots as a pdf file. The file will be saved in the working directory specified for the analysis. The default cut off for visualization is set at 15%, it can be changed to any value between 0-100%.
fingerprintplot( Individual_df, sample_info = NULL, cutoff = NULL, rowSplit = TRUE, Ref_group = NULL, show_ref_group = FALSE, Group_column = NULL, Aggregate = NULL, filename = NULL, height = NULL, width = NULL )
Individual_df |
Dataframe with output generated after running the 'Individualcomparison' function |
sample_info |
A dataframe with sample annotation. |
cutoff |
Numeric value specifying the percentage cut off used for fingerprint visualization ( 0 to 100). |
rowSplit |
Logical operator (TRUE/FALSE) to indicate if rows of the heatmaps should be split by each aggregate |
Ref_group |
Characters name of reference group or samples that considered as control |
show_ref_group |
Character vector specifying value within the group column that will be used as Reference group |
Group_column |
Name of the columns for the groups used for the analysis |
Aggregate |
Character vector specifying name of specific module aggregates for heatmap fingerprint plot |
filename |
Character vector with a name for saving file |
height |
Sets the height of the graphics region in inches. The default values are 28 |
width |
Sets the width of the graphics region in inches. The default values are 17 |
A heatmap of % of module response in each single sample
Darawan Rinchai drinchai@gmail.com
## data could be downloaded from ExperimentHub("GSE13015") library(ExperimentHub) library(SummarizedExperiment) dat = ExperimentHub() res = query(dat , "GSE13015") GSE13015 = res[["EH5429"]] Individual_df = Individualcomparison(GSE13015, sample_info = NULL, FC = 1.5, DIFF = 10, Group_column = "Group_test", Ref_group = "Control") fingerprintplot(Individual_df, sample_info = NULL, cutoff = 15, rowSplit = TRUE, Ref_group = "Control", show_ref_group = FALSE, Group_column = "Group_test", Aggregate = c("A28"), filename = tempfile(), height = 5, width = 10)