Hi,
I have been trying to generate a ridgeline plot based on some data from my recent experiment.
I ran several samples and want to generate a graphic in order to compare them. They are HPLC analysis and a ridgeline plot is probably the best approach to compare them.
I would like to create something similar to this graphic
When I create the plot, I obtain a similar profile for all the sample which makes no sense.
Here is my code:
> library(readxl)
> HPLC_Data <- read_excel("Desktop/R-studio presentation/Catalase inhibitor SA.xls",
+ sheet = "Formated", range = "A1:F49")
> View(HPLC_Data)
> library(ggplot2)
> library(ggridges)
> library(tidyr)
> library(reprex)
> library(datapasta)
> dim(HPLC_Data)
[1] 48 6
> gather(HPLC_Data, Sample, Absorbance, 2:6)
# A tibble: 240 x 3
Time Sample Absorbance
<dbl> <chr> <dbl>
1 3.09 Control 16H 2965
2 3.10 Control 16H 2830
3 3.10 Control 16H 2624
4 3.11 Control 16H 2763
5 3.12 Control 16H 3126
6 3.12 Control 16H 2947
7 3.13 Control 16H 3046
8 3.13 Control 16H 2845
9 3.14 Control 16H 3039
10 3.15 Control 16H 2472
# … with 230 more rows
> HPLC_Data_Long <- gather(HPLC_Data, Sample, Absorbance, 2:6)
> ggplot(HPLC_Data_Long, aes(x = Time, y = Sample)) + geom_density_ridges()
Picking joint bandwidth of 0.0345
> reprex::reprex()
Removing leading prompts from reprex source.
Rendering reprex...
Error: callr subprocess failed: <text>:20:13: unexpected '='
19: HPLC_Data <- read_excel("Desktop/R-studio presentation/Catalase inhibitor SA.xls",
20: + sheet =
And here is the graph generated, all profiles are similar but they should be different
I cannot understand, which information/command is missing.
Or do I need to mention "Absorbance" as y and group my samples?
Here is a sample data set:
After generating this data sample, I notice my values are followed with a "L", e.g. "2054L", is it the reason why I cannot generate a correct plot?
HPLC_Data <- tibble::tribble(
~Time, ~Control.16H, ~`0.05mM.16H`, ~`0.1mM.16H`, ~`0.5mM.16H`, ~`1mM.16H`, ~`5.mM.16H`,
3.093, 2965L, 1409L, 2054L, 1380L, 1795L, 1135L,
3.099, 2830L, 1584L, 2278L, 1386L, 2232L, 1411L,
3.105, 2624L, 1574L, 2209L, 1232L, 1771L, 1331L,
3.111, 2763L, 1460L, 2294L, 1348L, 1969L, 1035L,
3.117, 3126L, 1467L, 2342L, 1386L, 1615L, 1370L,
3.123, 2947L, 1568L, 2354L, 1383L, 1924L, 1336L,
3.129, 3046L, 1533L, 2108L, 1327L, 1787L, 1364L,
3.134, 2845L, 1625L, 2371L, 1321L, 1674L, 1287L,
3.14, 3039L, 1615L, 2315L, 1293L, 2197L, 1276L,
3.146, 2472L, 1621L, 2310L, 1137L, 1891L, 1034L,
3.152, 2654L, 1304L, 2292L, 1491L, 1703L, 1136L,
3.158, 2489L, 1492L, 2249L, 1302L, 1689L, 1413L,
3.164, 2788L, 1482L, 2358L, 1388L, 1864L, 1376L,
3.17, 2745L, 1625L, 2239L, 1290L, 1804L, 1043L,
3.176, 2769L, 1477L, 2231L, 1125L, 2304L, 1296L,
3.182, 2813L, 1655L, 2516L, 1384L, 1909L, 1251L,
3.188, 2648L, 1388L, 2185L, 1330L, 1926L, 1420L,
3.194, 2900L, 1383L, 2189L, 838L, 1894L, 1213L,
3.2, 3242L, 1465L, 2310L, 1280L, 1600L, 1372L,
3.206, 2949L, 1675L, 2079L, 1212L, 1970L, 1329L,
3.212, 2644L, 1354L, 2282L, 1290L, 2169L, 1239L,
3.218, 2951L, 1302L, 2722L, 1146L, 1771L, 1390L,
3.223, 2637L, 1442L, 2011L, 1154L, 1603L, 1116L,
3.229, 2688L, 1398L, 2540L, 1289L, 1925L, 1330L,
3.235, 3140L, 1466L, 2329L, 1465L, 1712L, 1337L,
3.241, 3341L, 1151L, 2084L, 1431L, 1669L, 1288L,
3.247, 2843L, 1406L, 2116L, 1317L, 1618L, 1265L,
3.253, 2287L, 1693L, 2514L, 1210L, 1762L, 1192L,
3.259, 2312L, 1343L, 2014L, 968L, 1552L, 1237L,
3.265, 2266L, 1315L, 1662L, 1056L, 1550L, 1018L,
3.271, 1775L, 1067L, 1380L, 769L, 1015L, 657L,
3.277, 1276L, 709L, 1210L, 582L, 956L, 509L,
3.283, 1202L, 688L, 903L, 221L, 456L, 303L,
3.289, 1010L, 206L, 653L, 194L, 348L, 309L,
3.295, 576L, 184L, 544L, 236L, 257L, 0L,
3.301, 517L, 0L, 327L, 183L, 164L, 0L,
3.307, 485L, 187L, 348L, 161L, 306L, 272L,
3.313, 615L, 188L, 381L, 212L, 247L, 234L,
3.318, 461L, 244L, 360L, 202L, 268L, 282L,
3.324, 549L, 217L, 481L, 203L, 182L, 280L,
3.33, 537L, 0L, 387L, 214L, 292L, 211L,
3.336, 354L, 235L, 328L, 250L, 245L, 243L,
3.342, 344L, 233L, 335L, 0L, 257L, 218L,
3.348, 473L, 0L, 437L, 0L, 281L, 213L,
3.354, 474L, 0L, 228L, 200L, 311L, 193L,
3.36, 414L, 274L, 370L, 229L, 205L, 202L,
3.366, 335L, 185L, 285L, 207L, 316L, 277L,
3.372, 507L, 161L, 321L, 226L, 327L, 172L,
3.378, 285L, 236L, 498L, 259L, 383L, 173L,
3.384, 477L, 202L, 179L, 241L, 253L, 210L,
3.39, 336L, 0L, 251L, 191L, 0L, 167L
)
head(HPLC_Data)
#> # A tibble: 6 x 7
#> Time Control.16H `0.05mM.16H` `0.1mM.16H` `0.5mM.16H` `1mM.16H` `5.mM.16H`
#> <dbl> <int> <int> <int> <int> <int> <int>
#> 1 3.09 2965 1409 2054 1380 1795 1135
#> 2 3.10 2830 1584 2278 1386 2232 1411
#> 3 3.10 2624 1574 2209 1232 1771 1331
#> 4 3.11 2763 1460 2294 1348 1969 1035
#> 5 3.12 3126 1467 2342 1386 1615 1370
#> 6 3.12 2947 1568 2354 1383 1924 1336
Thank you for your help.
