search

hms-dbmi / UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
https://cran.rstudio.com/web/packages/UpSetR
Other
763 stars 156 forks source link

number of sets #248

Open antoine4ucsd opened 1 year ago

antoine4ucsd commented 1 year ago

Hello I found this package very interesting to plot my data of reported symptoms. my data include daily report of ~30 symptoms across 5 participants. image

I ran this code with all the symptoms but get this error

mydata %>% 
        UpSetR::upset(
                sets = c("Malaise", "Back Pain", "Joint Pain", "Muscle Pain", "Fever", 
                         "Anorexia", "Nausia", "Bloating", "Epigastric Pain", "Trouble Swallowing", 
                         "Skin Rash", "Weakness", "Confusion", "Delirium", "Agitation", 
                         "Headache", "Abdominal Pain", "Gingival Bleeding", "Nasal Bleeding", 
                         "Asthenia", "Cough", "Nasal Congestion", "Constipation", "Arthralgia", 
                         "Lips Swelling", "Sore Throat", "Hypoglycemia", "Altered Consciousness", 
                         "Convulsions", "Gastric Bleeding", "Oral Bleeding", "Haemorragic Conjunctivitis"
                ),
                order.by = "freq",
                sets.bar.color = c("#aab6b9", "#7cbecc", "#7cbecc", "#7cbecc", "#aab6b9", "#2b9f84", 
                                            "#2b9f84", "#2b9f84", "#2b9f84", "#2b9f84", "#aab6b9", "#7cbecc", 
                                            "#ffdd73", "#ffdd73", "#ffdd73", "#aab6b9", "#2b9f84", "#d4595d", 
                                            "#d4595d", "#aab6b9", "#aab6b9", "#aab6b9", "#2b9f84", "#7cbecc", 
                                            "#aab6b9", "#aab6b9", "#aab6b9", "#ffdd73", "#ffdd73", "#d4595d", 
                                            "#d4595d", "#d4595d"), # optional colors
                                            empty.intersections = "on",
                #nintersects = 5,
                #nsets = 5, 
                number.angles = 0,
                point.size = 3.5,
                line.size = 2, 
                mainbar.y.label = "Symptoms Combinations",
                sets.x.label = "Patients with Symptom")
Error: vector memory exhausted (limit reached?)

my dataframe is 57x37 size

I also tried with nintersets=5 but still same error. is there a way to include all symptoms in the analyses even when only plotting the top N combinations?

thank you!