r,ggplot2,dplyr,tidyr , Plotting (ggplot) numeric values from mixed long format column of class character

Plotting (ggplot) numeric values from mixed long format column of class character


Tag: r,ggplot2,dplyr,tidyr

Following the tidy data standard, I have my data in long format with a key and a value column. The values for some keys are numeric, for others are characters, and so R has the entire column set as character class.

When I use filter() to pipe only the numeric data to ggplot (data with key 'a' is numeric), and then use as.numeric() on the value definition, it does not convert correctly - I see to just get sequence numbers instead of values. What am I doing wrong?

filter(data, measure == "a") %>% 
  ggplot(aes(x = as.numeric(value), 
             x = as.factor(subject_instance), 
             color = as.factor(subject_instance))) + 

What is the best way to handle mixed classes in long format (i.e. is it other than the way I'm doing it).


How to I get ggplot to convert to numeric correctly?

Workable example (sample of 40 rows from larger set):

    mydata <- structure(list(ResponseID = c("R_40LUIW7O8Lnj7Cd", "R_aXo4IXJ2eRTyThr", 
"R_9sHFiKGtn4ZhNiJ", "R_0BMN3JynUPiB0dn", "R_9mqmDcAKzae6ko5", 
"R_4T7qN9appsgbnxj", "R_5BeXW1ygKISxISV", "R_3JJY4UGvbzzDYTX", 
"R_0AN81Cdgz7ncPDD", "R_aXo4IXJ2eRTyThr", "R_40LUIW7O8Lnj7Cd", 
"R_8BOtUltxr8O6AeN", "R_40LUIW7O8Lnj7Cd", "R_1KUj25KpGbKOaGh", 
"R_5BeXW1ygKISxISV", "R_0AN81Cdgz7ncPDD", "R_aXo4IXJ2eRTyThr", 
"R_aXo4IXJ2eRTyThr", "R_0N8LUMfEP12P4Wh", "R_0wuddsG9KJhHkRn", 
"R_1R3kGCm3vPWi4dL", "R_50W5K8wp8m1yOZ7", "R_0wuddsG9KJhHkRn", 
"R_ctKujSc0Zr5fldz", "R_4SDzTFmolPaB8wt", "R_0Ng4gEnCnkCTuoB", 
"R_0Ng4gEnCnkCTuoB", "R_eb5LkAh0nBVqc9n", "R_0vqNorszrDGN6MB", 
"R_40LUIW7O8Lnj7Cd", "R_6s1Q2hFaqRLMKKF", "R_8BOtUltxr8O6AeN", 
"R_4SDzTFmolPaB8wt", "R_3JJY4UGvbzzDYTX", "R_3JJY4UGvbzzDYTX", 
"R_77mJUnh0OPtvCEl", "R_bxtLgQnlf4iaCWx", "R_6s1Q2hFaqRLMKKF", 
"R_7X8L8LwKo6UdWgR", "R_9mqmDcAKzae6ko5"), ID = c("R_3I0G7xzqlA4lUmm", 
"R_12m5J3hXrv8ObMa", "R_3PmEIrRgCUr0X3L", "R_YQuCAn43cgRMHy9", 
"R_51GdFWDnxQ7zvpv", "R_x9g4FVQzeqAJG8h", "R_QmDHvIxNJUypJip", 
"R_2cuyzZ8C4khOGs8", "R_3fUUNvffCN7GUrn", "R_12m5J3hXrv8ObMa", 
"R_3I0G7xzqlA4lUmm", "R_xgbhYoALaqQ9TDX", "R_3I0G7xzqlA4lUmm", 
"R_28I21bSyxgRcyGo", "R_QmDHvIxNJUypJip", "R_3fUUNvffCN7GUrn", 
"R_12m5J3hXrv8ObMa", "R_12m5J3hXrv8ObMa", "R_9L8RxssmQOGrPAR", 
"R_3iExjba1az5mpLw", "R_2wodtnGyQkaGTbX", "R_dnln2Bzdjahd3ax", 
"R_3iExjba1az5mpLw", "R_29gE0fK7dB6HENJ", "R_2E0mBlZmT618zQp", 
"R_3EVZt1ncuzTbVRr", "R_3EVZt1ncuzTbVRr", "R_2anUpVhXXReyZAX", 
"R_1dz55WFaXZ3Lm3Y", "R_3I0G7xzqlA4lUmm", "R_vUJsBPPRxV9J6CJ", 
"R_xgbhYoALaqQ9TDX", "R_2E0mBlZmT618zQp", "R_2cuyzZ8C4khOGs8", 
"R_2cuyzZ8C4khOGs8", "R_3LYcR4i5YB2k0N0", "R_yL9qi0TMXHfuJK9", 
"R_vUJsBPPRxV9J6CJ", "R_1DqckuFAYHkKjDg", "R_51GdFWDnxQ7zvpv"
), icon = c(".rprt", ".mddm", ".cnsl", "ord.cnsl", "sgn.alrt", 
"ent.advr", "flg.lab2", "ord.lab2", ".mddm", ".mds2", "rmv.prb2", 
"sch.imgn", "edt.not2", "edt.prb4", "ord.lab", "grp.lab", "src.note", 
"sgn.alrt", "sgn.imgn", "sch.lab", "sch.lab", ".note", "viw.imgn", 
"flg.lab2", ".mddm", "ent.prbl", "ent.vtls", "ord.med", ".hstr", 
"rnw.alrt", "ent.vtls", "viw.vtls", "sch.lab2", "edt.note", "rnw.med", 
"ord.prcd", "rmv.prbl", "crt.grph", "edt.prb3", "ent.prb2"), 
    measure = c("firstclick", "lastclick", "subject", "clickcount", 
    "pagesubmit", "firstclick", "subject", "lastclick", "subject", 
    "pagesubmit", "firstclick", "subject", "clickcount", "lastclick", 
    "clickcount", "firstclick", "pagesubmit", "pagesubmit", "pagesubmit", 
    "lastclick", "action", "clickcount", "firstclick", "clickcount", 
    "subject", "clickcount", "firstclick", "lastclick", "subject", 
    "pagesubmit", "action", "lastclick", "lastclick", "pagesubmit", 
    "clickcount", "firstclick", "firstclick", "action", "pagesubmit", 
    "subject"), value = c("2.602", "4.849", "Consult(s)", "6", 
    "180", "1.456", "Lab / Imaging / Diagnostic", "70.335", "Medication(s)", 
    "180", "1.133", "Lab / Imaging / Diagnostic", "4", "3.938", 
    "4", "3.003", "180", "180", "180", "20.519", "Schedule", 
    "4", "4.758", "4", "Medication(s)", "4", "1.706", "8.582", 
    "Patient history", "11.599", "Enter", "9.098", "11.897", 
    "180", "4", "1.728", "2.423", "Search", "180", "Problem(s)"
    ), file = structure(c(60L, 37L, 4L, 41L, 67L, 17L, 25L, 44L, 
    37L, 39L, 57L, 63L, 11L, 15L, 43L, 29L, 66L, 67L, 68L, 64L, 
    64L, 40L, 78L, 25L, 37L, 20L, 22L, 45L, 33L, 58L, 22L, 87L, 
    65L, 10L, 59L, 47L, 56L, 7L, 14L, 21L), .Label = c("alert.png", 
    "allergies.png", "check-order.png", "consult.png", "copy-graph.png", 
    "create-encounter.png", "create-graph.png", "create-note.png", 
    "create-report.png", "edit-note.png", "edit-note2.png", "edit-problem.png", 
    "edit-problem2.png", "edit-problem3.png", "edit-problem4.png", 
    "encounter.png", "enter-adverse.png", "enter-med.png", "enter-medadmin.png", 
    "enter-problem.png", "enter-problem2.png", "enter-vitals.png", 
    "flag-imaging.png", "flag-lab.png", "flag-lab2.png", "flag-order.png", 
    "followup.png", "forward-alert.png", "graph-lab.png", "graph-lab2.png", 
    "graph-vitals.png", "graph.png", "history.png", "imaging.png", 
    "lab1.png", "lab2.png", "medadmin.png", "meds1.png", "meds2.png", 
    "note.png", "order-consult.png", "order-imaging.png", "order-lab.png", 
    "order-lab2.png", "order-med.png", "order-med2.png", "order-procedure.png", 
    "order-procedure2.png", "order.png", "problem1.png", "problem2.png", 
    "procedure1.png", "procedure2.png", "refill-med.png", "refill-med2.png", 
    "remove-problem.png", "remove-problem2.png", "renew-alert.png", 
    "renew-med.png", "report.png", "schedule-consult.png", "schedule-followup.png", 
    "schedule-imaging.png", "schedule-lab.png", "schedule-lab2.png", 
    "search-note.png", "sign-alert.png", "sign-imaging.png", 
    "sign-lab.png", "sign-lab2.png", "sign-note.png", "sign-order.png", 
    "sign-report.png", "sort-alert.png", "sort-vitals.png", "view-adverse.png", 
    "view-history.png", "view-imaging.png", "view-lab.png", "view-lab2.png", 
    "view-med.png", "view-note.png", "view-order.png", "view-problem.png", 
    "view-problem2.png", "view-report.png", "view-vitals.png", 
    "vitals.png"), class = "factor"), icon_action = c("", "", 
    "", "order", "sign", "enter", "flag", "order", "", "", "remove", 
    "schedule", "edit", "edit", "order", "graph", "search", "sign", 
    "sign", "schedule", "schedule", "", "view", "flag", "", "enter", 
    "enter", "order", "", "renew", "enter", "view", "schedule", 
    "edit", "renew", "order", "remove", "create", "edit", "enter"
    ), icon_subject = c("report", "medadmin", "consult", "consult", 
    "alert", "adverse", "lab2", "lab2", "medadmin", "meds2", 
    "problem2", "imaging", "note2", "problem4", "lab", "lab", 
    "note", "alert", "imaging", "lab", "lab", "note", "imaging", 
    "lab2", "medadmin", "problem", "vitals", "med", "history", 
    "alert", "vitals", "vitals", "lab2", "note", "med", "procedure", 
    "problem", "graph", "problem3", "problem2"), instance = structure(c(2L, 
    8L, 7L, 26L, 80L, 49L, 78L, 24L, 11L, 7L, 83L, 24L, 77L, 
    43L, 26L, 67L, 73L, 38L, 31L, 74L, 27L, 12L, 26L, 87L, 15L, 
    31L, 53L, 42L, 2L, 53L, 88L, 57L, 47L, 62L, 54L, 37L, 40L, 
    78L, 32L, 33L), .Label = c("1", "2", "3", "4", "5", "6", 
    "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", 
    "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", 
    "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", 
    "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", 
    "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", 
    "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", 
    "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", 
    "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", 
    "87", "88"), class = "factor"), action_instance = c(NA, NA, 
    NA, 2L, 7L, 3L, 4L, 1L, NA, NA, 2L, 1L, 5L, 2L, 2L, 2L, 1L, 
    6L, 2L, 4L, 1L, NA, 2L, 4L, NA, 2L, 3L, 4L, NA, 1L, 6L, 9L, 
    1L, 5L, 2L, 2L, 1L, 3L, 2L, 1L), subject_instance = c(1L, 
    1L, 1L, 2L, 4L, 2L, 7L, 2L, 1L, 1L, 3L, 2L, 1L, 1L, 1L, 6L, 
    5L, 3L, 2L, 3L, 2L, 1L, 2L, 7L, 1L, 2L, 4L, 2L, 1L, 5L, 5L, 
    3L, 4L, 4L, 3L, 1L, 3L, 3L, 1L, 2L)), .Names = c("ResponseID", 
"ID", "icon", "measure", "value", "file", "icon_action", "icon_subject", 
"instance", "action_instance", "subject_instance"), class = c("tbl_df", 
"data.frame"), row.names = c(NA, -40L))

filter(mydata, measure=="pagesubmit") %>% ggplot(aes(y=as.numeric(value), x=as.factor(subject_instance), color=as.factor(subject_instance))) + geom_boxplot()

Also, on an semi-related note, why doesn't this work?:

filter(icon, measure=="pagesubmit") %>% mean(value)


As mentioned by @Spacedman, you example is not reproducible/consistent.

Part 1

This works:

filter(mydata, measure == "pagesubmit") %>% 
    y = as.numeric(value), 
    x = as.factor(subject_instance), 
    color = as.factor(subject_instance))) + 

Part 2

If you want the mean of all measure equal to pagesubmit, you can do:

filter(mydata, measure == "pagesubmit") %>% 
  summarise(mean = mean(as.numeric(value)))

Your initial attempt does not work because you are trying to take the mean() out of the whole data frame. In fact, when you do ... %>% mean(value) you get the following error message:

# Warning message:
# In mean.default(., value) : argument is not numeric or logical: returning NA

Where . is the left-hand argument (mydata filtered to retain only measure equal to pagesubmit) that %>% pipes forward to mean(). Following the same logic you should instead do:

mydata %>% 
  filter(measure == "pagesubmit") %>%
  .$value %>% ## extract a character vector of values
  as.numeric() %>% ## convert it to numeric
  mean() ## calculate the mean


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I have quite a simple dataset: ID Value Time 1 censored 1 1 censored 2 1 uncensored 3 1 uncensored 4 1 censored 5 1 censored 6 2 censored 1 2 uncensored 2 2 uncensored 3 2 uncensored 4 2 censored 5 I want to keep the first uncensored occurrence,...

Aggregating data in R

user_id date datetime page 217568 6/12/2015 49:23.9 Vodafone | How to get in touch with Vodafone 135437 6/10/2015 43:35.7 My Vodafone – Manage your Vodafone Pay Monthly Account Online – Vodafone 196094 6/13/2015 33:39.4 Check the status of Vodafone’s mobile network in real-time 74197 6/6/2015 52:46.1 undefined 153501 6/5/2015 02:55.5...

Limit the color variation in R using scale_color_grey

Before I start, allow me to explain my graph: I have two Genotypes (WTB and whd) and each have two conditions (0 and 7), so I have four lines. Now, I want to make a plot where each variable and its condition is the same color. Anything with whd will...

how to get values from selectInput with shiny

I am playing around with the shiny packages for some hours now, and wanted to make a select input widget that enables me to download a certain data set from the server. So i figured out a way to get me this data frame containing all my IDs for downloading:...

Convert strings of data to “Data” objects in R [duplicate]

This question already has an answer here: as.Date with dates in format m/d/y in R 2 answers My problem is that the as.Date function does not convert the values in a "date" column of a data frame into Date objects. I have a data.frame nmmaps. Here is a short...

How can I minimize this function in R?

I'm attempting to write a formula that will determine a value of a that minimizes the function output myfun (i.e. a-fptotal). MWE: c <- as.matrix(c(.25,.5,.25)) d <- as.matrix(c(10000,12500,15000)) e <- 700 f <- 1.1 tr <- .30 myfun <- function(a) { b <- max(a-e,0) df <- data.frame(u1=c(c*b*.40),u2=c(c*b*.60)) df$year <- 1:nrow(df)...

Using R to Assign Treatments to Groups

We have seven exposures and 24 groups. We would like to randomly assign five of the seven exposures to groups while also ensuring that we end up with a consistent count for each exposure, meaning that each exposure ends up being exposed about the same number of times. I have...

ggplot2 & facet_wrap - eliminate vertical distance between facets

I'm working with some data that I want to display as a nxn grid of plots. Edit: To be more clear, there's 21 categories in my data. I want to facet by category, and have those 21 plots in a 5 x 5 square grid (where the orphan is by...

Find multiple consecutive empty lines

I'm trying to chop up a text file into the articles it contains. Usually this is done by identifying a pattern each article begins with. Unfortunately the database I downloaded the articles from doesn't have that. The only pattern I can find is that after each article there are 3...

Fitting a subset model with just one lag, using R package FitAR

I am trying to fit a subset model with only lag 4. In the manual it's written "you must use p=c(0,0,0,4) since p=4 will fit a full AR(4)". I did this. #fit a subset model with just lag 4 Fit=FitAR(p=c(0,0,0,4), lag.max = "default", ARModel = "ARz") However, I get the...