ggplot line graph shows overlap for discrete Y axis variable - r

I am trying to plot a time series plot using ggplot. I have a discrete variable that just describes if a vehicle engine was on or off through a given time.
Naturally, it should either be 0 or 1, there can't be an overlap. But as seen in the below plot, there's a considerable overlap.
I am pretty new to ggplot. Could someone please let me know what the issue is.
The code I am using is:
pd %>%
ggplot(aes(x = SampleTime, y = as.factor(Value))) + geom_line(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
structure of data:
str(pd)
'data.frame': 474 obs. of 2 variables:
$ SampleTime: POSIXct, format: "2020-11-30 00:17:46" "2020-11-30 01:17:47" "2020-11-30 02:17:48" "2020-11-30 03:17:49" ...
$ Value : num 0 0 0 0 0 0 0 0 0 1 ...
data used:
structure(list(SampleTime = structure(c(1606675666, 1606679267,
1606682868, 1606686469, 1606690070, 1606693671, 1606697271, 1606700872,
1606704473, 1606706974, 1606707066, 1606707129, 1606707192, 1606707255,
1606707318, 1606707382, 1606707445, 1606707508, 1606707571, 1606707631,
1606707694, 1606707754, 1606707817, 1606707880, 1606707943, 1606708006,
1606708069, 1606708132, 1606708195, 1606708258, 1606708318, 1606708381,
1606708441, 1606708504, 1606708567, 1606708630, 1606708691, 1606708751,
1606708814, 1606708877, 1606708940, 1606709003, 1606709066, 1606709129,
1606709192, 1606709255, 1606709318, 1606709381, 1606709444, 1606709507,
1606709570, 1606709633, 1606709696, 1606709759, 1606709822, 1606709885,
1606709948, 1606710011, 1606710074, 1606710137, 1606710200, 1606710263,
1606710348, 1606710411, 1606710474, 1606710537, 1606710600, 1606710663,
1606710726, 1606710789, 1606710852, 1606710915, 1606710978, 1606711041,
1606711104, 1606711167, 1606711230, 1606711293, 1606711356, 1606711419,
1606711482, 1606711545, 1606711608, 1606711671, 1606711734, 1606711797,
1606711860, 1606711923, 1606711986, 1606712049, 1606712112, 1606712175,
1606712238, 1606712301, 1606712365, 1606712428, 1606712491, 1606712553,
1606712617, 1606712679, 1606712756, 1606712909, 1606712970, 1606713007,
1606713034, 1606713094, 1606713157, 1606713220, 1606713283, 1606713346,
1606713409, 1606713472, 1606713535, 1606713598, 1606713661, 1606713724,
1606713787, 1606713850, 1606713913, 1606713976, 1606714039, 1606714102,
1606714165, 1606714228, 1606714291, 1606714354, 1606714417, 1606714480,
1606714543, 1606714606, 1606714669, 1606714732, 1606714795, 1606714858,
1606714921, 1606714984, 1606715047, 1606715110, 1606715173, 1606715236,
1606715299, 1606715362, 1606715425, 1606715488, 1606715551, 1606715614,
1606715677, 1606715740, 1606715803, 1606715866, 1606715929, 1606715992,
1606716055, 1606716118, 1606716181, 1606716244, 1606716307, 1606716370,
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1606717075, 1606717138, 1606717201, 1606717264, 1606717327, 1606717390,
1606717453, 1606717516, 1606717579, 1606717642, 1606717705, 1606717768,
1606717831, 1606717894, 1606717957, 1606718021, 1606718084, 1606718147,
1606718210, 1606718273, 1606718336, 1606718399, 1606718462, 1606718525,
1606718588, 1606718651, 1606718714, 1606718777, 1606718839, 1606718903,
1606718965, 1606719029, 1606719091, 1606719155, 1606719218, 1606719281,
1606719344, 1606719407, 1606719470, 1606719533, 1606719596, 1606719659,
1606719722, 1606719785, 1606719848, 1606719911, 1606719974, 1606720037,
1606720100, 1606720163, 1606720226, 1606720289, 1606720352, 1606720415,
1606720478, 1606720498, 1606721559, 1606721619, 1606721682, 1606721745,
1606721808, 1606721871, 1606721934, 1606721997, 1606722060, 1606722123,
1606722186, 1606722249, 1606722312, 1606722375, 1606722438, 1606722501,
1606722564, 1606722627, 1606722690, 1606722753, 1606722816, 1606722858,
1606722892, 1606722952, 1606723015, 1606723078, 1606723141, 1606723204,
1606723267, 1606723330, 1606723393, 1606723456, 1606723519, 1606723582,
1606723645, 1606723708, 1606723771, 1606723834, 1606723897, 1606723960,
1606724023, 1606724086, 1606724149, 1606724212, 1606724275, 1606724338,
1606724401, 1606724464, 1606724527, 1606724590, 1606724653, 1606724716,
1606724779, 1606724842, 1606724905, 1606724968, 1606725031, 1606725094,
1606725157, 1606725220, 1606725283, 1606725346, 1606725409, 1606725472,
1606725535, 1606725598, 1606725661, 1606725721, 1606725784, 1606725840,
1606729441, 1606730753, 1606730814, 1606730857, 1606731021, 1606731081,
1606731144, 1606731207, 1606731270, 1606731333, 1606731396, 1606731459,
1606731522, 1606731585, 1606731648, 1606731711, 1606731774, 1606731837,
1606731900, 1606731963, 1606732026, 1606732089, 1606732138, 1606732956,
1606733017, 1606733080, 1606733143, 1606733206, 1606733269, 1606733332,
1606733395, 1606733458, 1606733521, 1606733584, 1606733647, 1606733710,
1606733773, 1606733836, 1606733899, 1606733962, 1606734025, 1606734088,
1606734151, 1606734203, 1606735128, 1606735189, 1606735252, 1606735315,
1606735378, 1606735441, 1606735504, 1606735567, 1606735630, 1606735683,
1606739285, 1606742885, 1606744969, 1606745030, 1606745093, 1606745156,
1606745219, 1606745282, 1606745345, 1606745408, 1606745471, 1606745534,
1606745597, 1606745660, 1606745723, 1606745786, 1606745849, 1606745912,
1606745975, 1606746038, 1606746101, 1606746164, 1606746370, 1606746433,
1606746496, 1606746559, 1606746702, 1606746736, 1606746765, 1606746828,
1606746891, 1606746954, 1606747017, 1606747077, 1606747140, 1606747203,
1606747266, 1606747329, 1606747392, 1606747455, 1606747518, 1606747581,
1606747644, 1606747707, 1606747770, 1606747833, 1606747896, 1606747959,
1606748022, 1606748085, 1606748145, 1606748206, 1606748269, 1606748332,
1606748395, 1606748458, 1606748521, 1606748584, 1606748647, 1606748707,
1606748770, 1606748833, 1606748896, 1606748959, 1606749022, 1606749085,
1606749148, 1606749211, 1606749274, 1606749337, 1606749400, 1606749463,
1606749526, 1606749589, 1606749652, 1606749715, 1606749778, 1606749841,
1606749904, 1606749967, 1606750030, 1606750093, 1606750156, 1606750219,
1606750282, 1606750345, 1606750408, 1606750471, 1606750534, 1606750597,
1606750657, 1606750720, 1606750781, 1606750841, 1606750904, 1606750967,
1606751030, 1606751084, 1606754686, 1606758287, 1606759153, 1606759213,
1606759276, 1606759339, 1606759402, 1606759465, 1606759528, 1606759592,
1606759654, 1606759718, 1606759780, 1606759843, 1606759906, 1606759969,
1606760032, 1606760096, 1606760159, 1606760222, 1606760285, 1606760348,
1606760411, 1606760474, 1606760537, 1606760600, 1606760663, 1606760726,
1606760788, 1606760851, 1606760914, 1606760977), class = c("POSIXct",
"POSIXt"), tzone = ""), Value = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1)), row.names = c(NA, -474L), class = "data.frame")


ggplot automatically connects the gaps between observations if you use geom_line. Try to use geom_point instead to see the gaps:
pd %>%
ggplot(aes(x = SampleTime, y = as.factor(Value))) +
geom_point(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
Alternatively, you can use geom_line but don't convert Value to a factor and use the numeric value instead. This way you can see the change from 0 to 1 more clearly:
pd %>%
ggplot(aes(x = SampleTime, y = Value)) +
geom_line(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
Lastly, a slightly more appropriate option for categorical data might be to use geom_step instead, which at least connects the two categories with a vertical line:
pd %>%
ggplot(aes(x = SampleTime, y = Value)) +
geom_step(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
If that doesn't suffice, check out this post on how to connect the lines between each consecutive dot per group via geom_segment.

Related

Create groups in data frame based upon whether next value reaches a threshold

I have df with a column diff_index.
I'd like to create a grouping column based on whether the next value is greater than a threshold x - if the next value is greater than x, then I want a new group.
So in this case, if the threshold is 100, the first 12 entries will be group 1, then since the 13th value is 3877, group 2 begins here, until we reach 1979, in which group 3 starts, etc.
A data.table solution would be ideal.
df=structure(list(diff_index = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 3877, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1,
1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1979, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 136, 1, 1, 1, 1, 97, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 2, 11905, 1, 1, 1, 2764, 1, 1, 1, 676, 1, 1, 1, 2,
1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 469, 1, 1,
2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1,
1, 1, 1, 1, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
8121, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1737, 1, 1, 1, 1, 1, 1, 1,
1, 681, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, NA)), row.names = c(NA,
-393L), class = "data.frame")

library(tidyverse)
df %>%
mutate(group = cumsum(diff_index > 100) + 1)
Or with data.table:
dt[,group:=cumsum(diff_index > 100) + 1]
diff_index group
1: 1 1
2: 1 1
3: 1 1
4: 1 1
5: 1 1
---
389: 1 11
390: 1 11
391: 1 11
392: 1 11
393: NA NA

poLCA in R is not executing. I am getting a weird error message

I'm pretty new to R and I'm encountering an error that I'm not sure why I'm getting. I'm running R Studio Version 1.3.959 on Windows 10 and trying to use the package poLCA.
Here is my code:
library(scatterplot3d)
library(MASS)
library(poLCA)
data <- read.csv(file.choose(), header = TRUE)
data[-3] <- lapply(data[-3],gsub,pattern = "1", replacement = "2", fixed = TRUE)
data[-3] <- lapply(data[-3],gsub,pattern = "0", replacement = "1", fixed = TRUE)
cols.num<- c("A", "B", "C", "D", "E")
data[cols.num] <- sapply(data[cols.num],as.numeric)
AMER_all <- data[which(data$SALES_LEVEL_1 == "AMERICAS"),]
AMER_ALL_LSA <- cbind("A", "B", "C", "D", "E")
AMER_less_1000 <- AMER_all[which(AMER_all$WALLET_BINS == "<$2k"),]
AMER_less_1000_LCA <- poLCA(AMER_ALL_LSA, data = AMER_less_1000, nclass = 3, graphs = TRUE)
This is the error that I'm getting -
Error in runif(R * K.j[j]) : invalid arguments
In addition: There were 50 or more warnings (use warnings() to see the first 50)
and when I look at the warning I get this:
In FUN(newX[, i], ...) : no non-missing arguments to max; returning -Inf
Any idea on why I'm getting this error? I'm wondering if its the version of R that I downloaded. I recently needed to reimage my laptop and download R and RStudio from fresh again..
Sample Data
structure(list(ï..COMPANY_ID = c("GUC_123",
"GUC_111", "GUC_112", "GUC_113", "GUC_114",
"GUC_115", "GUC_116", "GUC_117",
"GUC_118", "GUC_119", "GUC_120", "GUC_121",
"GUC_122", "GUC_123", "GUC_124",
"GUC_125", "GUC_126", "GUC_127",
"GUC_128", "GUC_129"), SALES_LEVEL_1 = c("AMERICAS",
"APJC__", "AMERICAS", "AMERICAS", "APJC__", "AMERICAS", "EMEAR-REGION",
"AMERICAS", "AMERICAS", "EMEAR-REGION", "AMERICAS", "AMERICAS",
"AMERICAS", "AMERICAS", "EMEAR-REGION", "AMERICAS", "AMERICAS",
"AMERICAS", "APJC__", "EMEAR-REGION"), WALLET_BIN = c("$1k-$15k",
"$15k-$50", "$1k-$15k", "$100k-$200k", "$1k-$15k", "$15k-$50",
"$1k-$15k", "$1k-$15k", "$15k-$50", "$15k-$50", "$1k-$15k", "$1k-$15k",
"$15k-$50", "$1k-$15k", "$1k-$15k", "$50k-$100k", "$50k-$100k",
"$15k-$50", "$50k-$100k", "$1k-$15k"), A = c(1,
1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1), B = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), C = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), D = c(2,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1), E = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), F = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), G = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), H = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1), I = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1), J = c(2,
1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 1, 1), K = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), L = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), M = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), N = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), O = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1), P = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1), row.names = c(NA,
20L), class = "data.frame")

It looks like the very silly issue is defining the formula without quotation marks as also noted in this answer:
library(poLCA)
data <- read.delim("https://pastebin.com/raw/TNJNCxkH")
data[,5:ncol(data)] <- lapply(data[,5:ncol(data)],gsub,pattern = "1", replacement = "2", fixed = TRUE)
data[,5:ncol(data)] <- lapply(data[,5:ncol(data)],gsub,pattern = "0", replacement = "1", fixed = TRUE)
data[,5:ncol(data)] <- sapply(data[,5:ncol(data)],as.numeric)
AMER_all <- data[which(data$SALES_LEVEL_1 == "AMERICAS"),]
AMER_ALL_LSA <- cbind(PB_1,PB_2,PB_3,PB_4,PB_5)~1
AMER_less_1000_LCA <- poLCA(AMER_ALL_LSA, data = AMER_all, nclass = 3, graphs = TRUE)
#Conditional item response (column) probabilities,
# by outcome variable, for each class (row)
#...
#=========================================================
#Fit for 3 latent classes:
#=========================================================
#number of observations: 1016
#number of estimated parameters: 17
#residual degrees of freedom: 14
#maximum log-likelihood: -1068.675
#AIC(3): 2171.351
#BIC(3): 2255.052
#G^2(3): 1.362823 (Likelihood ratio/deviance statistic)
#X^2(3): 0.7509686 (Chi-square goodness of fit)
#
#ALERT: iterations finished, MAXIMUM LIKELIHOOD NOT FOUND

ComplexHeatmap - Highlight specific values in a heatmap

I'm using the ComplexHeatmap package in R to plot a matrix.
I would like to plot cells with specific values in different colors such as:
Red if value < threshold_low
Yellow if threshold_low < value < threshold_high
Green gradient if threshold_high < value < 0.9
White if value > 0.9
The code below produces something close to what I'm trying to achieve but not exactly...
There should be 3 values highlighted in 'red' (only are shown).
The legend doesn't show the red value.
I've tried different values in colorRamp2() but I still achieve the results I want.
Link to the package: https://github.com/jokergoo/ComplexHeatmap
Relevant documentation: https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/ComplexHeatmap/inst/doc/ComplexHeatmap.html
Reproducible example:
library(ComplexHeatmap)
library(circlize)
library(RColorBrewer)
mat <- structure(c(1, 0.154616894313456, 0.168336307012768, 1, 1, 0.453975613676526,
1, 1, 1, 1, 0.00056792615275985, 1, 1, 1, 1, 1, 0.105149642433548,
0.425158360263792, 1, 1, 0.501057722133202, 1, 1, 1, 0.00278294210196398,
1, 0.168271031634512, 1, 0.830063213792425, 1, 1, 1, 1, 1, 1,
1, 1, 1, 0.451156419955746, 1, 0.0274775797365075, 1, 1, 0.717017044202449,
1, 1, 1, 0.717321290931695, 0.0845704812428829, 1, 0.0699956751028108,
1, 0.275329648641519, 1, 0.0201980178890521, 0.0455613967501329,
1, 1, 0.536035636664544, 1, 1, 1, 1, 0.358910397894989, 1, 1,
1, 1, 1, 0.0467579359404697, 0.100390014456881, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 0.00196501415273741, 1, 1, 1, 1, 1, 1, 1, 1, 1,
0.52718575076658, 0.589648919728843, 0.016642521684359, 1, 1,
0.100523837174713, 0.62858401844093, 1, 1, 1, 0.00272095544860866,
1, 0.00152884219028376, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.00715615768151061,
1, 1, 0.0017044025565658, 1, 0.900838683850751, 1, 0.00286177891699905,
0.964009307250068, 1, 1, 1, 1, 0.712505373834541, 0.156595117903911,
0.698630689400136, 0.0497797620046933, 0.0432669236844255, 1,
0.482930753871518, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.863198034258964,
0.0914794415922655, 1, 1, 1, 1, 1, 0.130770966476073, 0.133939889164611,
1, 0.357244624441367, 0.0574932940137384, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 0.10152332525958, 1, 1, 1, 1, 1, 1, 1,
0.613891861387759, 1, 1, 1, 1, 0.0194347260355869, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.836989723814452,
0.262496570009738, 0.0266926025635128, 1, 1, 1, 0.409918984740791,
1, 1, 1, 0.000826603369076878, 0.251385649690035, 0.262496570009738,
1, 0.636285376736921, 1, 1, 1, 0.131975914025068, 1, 0.302372382987271,
1, 0.829657680365184, 0.234804722298138, 1, 0.480189087472427,
1, 1, 0.434351639718704, 1, 1, 1, 1, 1, 1, 1, 1, 0.827162805570832,
1, 0.000754621951469572, 1, 1, 1, 0.0607557227589793, 0.0466844602596043,
0.166584131048057, 1, 0.00375850252234914, 1, 0.00714919767503871,
1, 1, 0.0274923567061487, 0.317749204479313, 0.523992490899291,
0.0154308196673378, 1, 1, 1, 1, 0.283874713710679, 1, 1, 0.0879611832530085,
0.00614031465663928, 1, 0.44858333972042, 1, 1, 1, 1, 1, 1, 0.0999740979976858,
1, 0.0857648171802508, 0.129753363733359, 0.205913325652849,
0.164132124317898, 1, 1, 0.135339969223928, 0.441555384681617,
1, 1, 1, 0.619544298689775, 1, 1, 1, 1, 1, 0.00237701375005596,
1, 1, 0.149979241487463, 5.65028970245137e-06, 0.00435404367430347,
0.102437190438328, 0.159652054514079, 1.34807420832168e-05, 0.0781174367417338,
0.00168329325806749, 1, 1, 0.0178846842165573, 0.562000511433683,
1, 0.226033494133538, 1, 1, 1, 0.0116432115170938, 0.0158685033438527,
1, 1, 1, 1, 1, 0.226315459031352, 1, 0.0839844171448521, 0.00448638209236464,
0.741937003903222, 1, 1, 0.0969877781197935, 1, 1, 0.899533885687393,
0.11038695014775, 0.0691406897023532, 0.00864645807981477, 0.000409055625639548,
0.0432931123545735, 0.000183686382465392, 1, 1, 1, 1, 1, 0.262742531844371,
1, 0.695486348184785, 0.129359897480463, 0.7456928940893, 0.85934081881042,
1, 1, 1, 1, 1, 0.608552296219399, 1, 0.39067450494575, 1, 1,
1, 1, 0.411281105041672, 0.484196212791728, 0.198292538014945,
0.677053068881975, 1, 1, 1, 0.0318317218601013, 1, 1, 0.791347998335414,
1, 1, 1, 1, 0.240600397196919, 0.135644227364626, 1, 1, 1, 8.78013264925257e-05,
0.259727834661945, 0.305025003277675, 0.0492101609648877, 1,
0.667608208227447, 0.15068985721195, 1, 0.00197605148651341,
0.194624037083573, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.0758606965055501,
1, 1, 1, 1, 0.146826771370067, 1, 0.0318317218601013, 1, 0.267193726901327,
1, 0.0214353975572249, 1, 1), .Dim = c(53L, 8L), .Dimnames = list( NULL, NULL))
threshold_low <- 0.00015
threshold_high <- 0.05
color_breaks <-c(0, threshold_low, threshold_high, 0.9)
my_palette <- c( "red",
"yellow",
colorRampPalette(rev(brewer.pal(8, "Greens")))(n = length(color_breaks)-3),
"white")
col_fun = colorRamp2(color_breaks, my_palette)
Heatmap(mat,
cluster_rows = FALSE,
show_column_names = FALSE, # We use colored anno_block instead
#clustering_distance_rows = "euclidean",
cluster_columns=FALSE,
col = col_fun,
# Legend
heatmap_legend_param = list(
title = "values", direction = "horizontal",
legend_width = unit(.25, "npc"),
at = c(threshold_low, threshold_high, .5),
labels = c("<0.00015" , "<0.05", '1')
),
# Cell separator
rect_gp = gpar(col = "lightgray", lwd = 1),
width=unit(0.6,'npc'),
)

Following is the color mapping function I created:
offset = 1e-10
col_fun = colorRamp2(c(0, 0.00015, 0.00015+offset, 0.05, 0.05+offset, 0.9, 0.9+offset, 1),
c("red", "red", "yellow", "yellow", "lightgreen", "darkgreen", "white", "white"))
The correspondence is
0 "red"
0.00015 "red"
0.00015+offset "yellow"
0.05 "yellow"
0.05+offset "lightgreen"
0.9 "darkgreen"
0.9+offset "white"
1 "white"
The thing is you have different color schema in different intervals, you need to be careful with the endpoints of each interval.

How can I write a simple classifier and generate a merged dataframe from it

I have a df like this;
>df[1:6,1:6]
> ABT.263 ABT.869 ABT.888 AC220 Afatinib Afatinib.rescreen.
> BT-20 1 1 1 1 0 1
> CAL-120 0 1 1 1 1 1
> CAL-51 1 1 1 1 1 1
> CAL-85-1 1 1 1 1 1 0
> DU-4475 0 1 1 1 1 1
> HCC1143 1 1 1 1 0 1
Basically, I want to extract 1's and 0's of each column's row name. Then put them into adjacent columns in a loop form.
Desired output is like this;
> final_df[1:6,1:4]
> ABT.263_1 ABT.263_0 ABT.869_1 ABT.869_0
> BT-20 CAL-120 BT-20 NA
> CAL-51 DU-4475 CAL-120
> CAL-85-1 CAL-51
> HCC1143 CAL-85-1
> DU-4475
> HCC1143
I can extract rownames of 0 cells and 1 cells separately with this;
value1 <- rownames(df)[which(df[,1] == 1)]
value0 <- rownames(df)[which(df[,1] == 0)]
However, failed to assign value1 and value0 vectors respectively in a df format with loops.
> dput(head(resp_tnbc, 20))
structure(list(ABT.263 = c(1, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1,
1, 1, 1, 1, 1), ABT.869 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1), ABT.888 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1), AC220 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 0,
1, 1, 1, 1, 1, 1, 1), Afatinib = c(0, 1, 1, 1, 1, 0, 1, 1, 1,
0, 1, 0, 1, 1, 1, 0, 1), Afatinib.rescreen. = c(1, 1, 1, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), AG.014699 = c(1, 1, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AICAR = c(1, 1, 1, 1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0), AKTinhibitorVIII = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), AMG.706 = c(1,
1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1), AP.24534 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AR.42 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AS601245 = c(1,
1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AS605240 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AT.7519 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ATRA = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), AUY922 = c(1,
1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AV.951 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), Axitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), AZD6244 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), AZD6244.1 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AZD6482 = c(0,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), AZD6482.1 = c(0,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), AZD7762 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AZD8055 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), BAY61.3606 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bexarotene = c(1,
1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bicalutamide = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bicalutamide.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BIRB0796 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0), BIX02189 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bleomycin = c(1,
1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1), Bleomycin.50uM. = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMN.673 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.345541 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.536924.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.708163 = c(1,
0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.708163.1 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), BMS.754807 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bosutinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bryostatin1 = c(1,
1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), BX.795 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BX.912 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), CAL.101 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), Camptothecin = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CAY10603 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CCT007093 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CCT018159 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), CEP.701 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Cetuximab = c(0,
1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1), CH5424802 = c(1,
1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1), CHIR.99021 = c(1,
1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1), CHIR.99021.1 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CI.1040 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Cisplatin = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CP466722 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CP724714 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CUDC.101 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CX.5461 = c(1,
0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1), Cytarabine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Dabrafenib = c(1,
0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), DMOG = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Docetaxel = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Doxorubicin = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EHT1864 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EKB.569 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), Elesclomol = c(1,
1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1), Embelin = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EpothiloneB = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Etoposide = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EX.527 = c(1,
1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), FH535 = c(1,
1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1), FK866 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), FMK = c(1, 1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), FR.180204 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), FTI.277 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GDC0941 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), GDC0941.rescreen. = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Gefitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1), Gemcitabine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GenentechCpd10 = c(1,
1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK.1904529A = c(1,
1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1), GSK.650394 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK1070916 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), GSK2126458 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK269962A.1 = c(1,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), GSK429286A = c(1,
1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK690693 = c(0,
1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0), GW.2580 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1), GW441756 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0), HG.6.64.1 = c(1,
1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), I.BET151 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), IOX2 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), IPA.3 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JNJ.26854165 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), JNK.9L = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JNKInhibitorVIII = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JQ1 = c(1, 1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JQ1.1 = c(1, 1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1), JQ12 = c(1, 1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JW.7.24.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.055 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.102 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.236 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.244 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.260 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.266 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.270 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KU.55933 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), LAQ824 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Lenalidomide = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), LFM.A13 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), LY317615 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Masitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Methotrexate = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Midostaurin = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), MitomycinC = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), MK.2206 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0), MLN4924 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), MP470 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), MPS.1.IN.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NG.25 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Nilotinib = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), NPK76.II.72.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NSC.207895 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NSC.87877 = c(1,
0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), NU.7441 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), Nutlin.3a = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NVP.BEZ235 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NVP.BHG712 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ObatoclaxMesylate = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Olaparib = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Olaparib.1 = c(1,
0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1), OSI.027 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), OSI.906 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), OSI.930 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), OSU.03012 = c(1,
1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PAC.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Pazopanib = c(1,
1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1), PD.0325901 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1), PD.0332991 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PD.173074 = c(1,
1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0), PF.4708671 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PF.562271 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), PFI.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PHA.793887 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Phenformin = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1), PI.103 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PIK.93 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), piperlongumine = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), PLX4720 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PLX4720.rescreen. = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PXD101.Belinostat = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), QL.X.138 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), QL.XI.92 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1), QL.XII.47 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), QS11 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), RDEA119 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), RDEA119.rescreen. = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), RO.3306 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1), rTRAIL = c(1,
0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1), Ruxolitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SB.505124 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), SB.715992 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), SB216763 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SB52334 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), SB590885 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SGC0946 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1), Shikonin = c(1,
1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SL0101.1 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SN.38 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SNX.2112 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), STF.62247 = c(1,
1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), T0901317 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TAK.715 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Tamoxifen = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Temozolomide = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), Temsirolimus = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TG101348 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Thapsigargin = c(1,
1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1), THZ.2.102.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), THZ.2.49 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Tipifarnib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), TL.1.85 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TL.2.105 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TPCA.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Trametinib = c(1,
1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), TubastatinA = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), UNC0638 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), UNC0638.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), UNC1215 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vinblastine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vinorelbine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vismodegib = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), VNLG.124 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vorinostat = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), VX.11e = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), VX.702 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), WZ3105 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), X.5Z..7.Oxozeaenol = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), X17.AAG = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), X5.Fluorouracil = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), X681640 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XAV939 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), XL.184 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), XL.880 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XMD13.2 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XMD14.99 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XMD15.27 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Y.39983 = c(1,
0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), YK4.279 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), YM155 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), YM201636 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Zibotentan.ZD4054 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ZM.447439 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ZSTK474 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), row.names = c("BT-20",
"CAL-120", "CAL-51", "CAL-85-1", "DU-4475", "HCC1143", "HCC1187",
"HCC1395", "HCC1937", "HCC2157", "HCC38", "HDQ-P1", "Hs-578-T",
"MDA-MB-231", "MDA-MB-436", "MDA-MB-468", "MFM-223"), class = "data.frame")

Not really sure, because I did not fully understand your desired output...
But here is a go using the data.table-package
#load library
library(data.table)
#first, create the sample data
#note, rownames are stored in their own column, 'row_name'
dt <- fread("row_name ABT.263 ABT.869 ABT.888 AC220 Afatinib Afatinib.rescreen.
BT-20 1 1 1 1 0 1
CAL-120 0 1 1 1 1 1
CAL-51 1 1 1 1 1 1
CAL-85-1 1 1 1 1 1 0
DU-4475 0 1 1 1 1 1
HCC1143 1 1 1 1 0 1")
#melt the data to long format, using the 'row_name'-column as identifier
dt.melt <- melt( dt, id.vars = "row_name" )
#now summarise, pasting together row_names by variable-value combination
dt.melt[, .( row = paste0( row_name, collapse = ";" ) ),
by = .( value = paste0( variable, "_", value ) ) ]
# value row
# 1: ABT.263_1 BT-20;CAL-51;CAL-85-1;HCC1143
# 2: ABT.263_0 CAL-120;DU-4475
# 3: ABT.869_1 BT-20;CAL-120;CAL-51;CAL-85-1;DU-4475;HCC1143
# 4: ABT.888_1 BT-20;CAL-120;CAL-51;CAL-85-1;DU-4475;HCC1143
# 5: AC220_1 BT-20;CAL-120;CAL-51;CAL-85-1;DU-4475;HCC1143
# 6: Afatinib_0 BT-20;HCC1143
# 7: Afatinib_1 CAL-120;CAL-51;CAL-85-1;DU-4475
# 8: Afatinib.rescreen._1 BT-20;CAL-120;CAL-51;DU-4475;HCC1143
# 9: Afatinib.rescreen._0 CAL-85-1

A base R solution with a list of vectors is also possible:
Code:
names <- names(df)
#
l1 <- list()
for(i in 1:length(df)){
l1[[i]] <- rownames(df)[which(df[,names[i]] == 1)]
}
Result
l1
[[1]]
[1] "BT-20" "CAL-51" "CAL-85-1" "HCC1143"
[[2]]
[1] "BT-20" "CAL-120" "CAL-51" "CAL-85-1" "DU-4475" "HCC1143"
[[3]]
[1] "BT-20" "CAL-120" "CAL-51" "CAL-85-1" "DU-4475" "HCC1143"
[[4]]
[1] "BT-20" "CAL-120" "CAL-51" "CAL-85-1" "DU-4475" "HCC1143"
[[5]]
[1] "CAL-120" "CAL-51" "CAL-85-1" "DU-4475"
[[6]]
[1] "BT-20" "CAL-120" "CAL-51" "DU-4475" "HCC1143"
This is the list of names with 1 in the data.frame, the list of 0's could be obtained identically.

How to plot a different colour depending on the value in geom_line ggplot

I have a ggplot like so:
I would like to have a line that is red if it is above the topmost geom_hline, preferably only when it is above the line. Failing this geom_point colour change will do:
The minimal dataset
structure(list(chr = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1), leftPos = c(480000, 600000, 2520000, 2760000, 2880000,
3000000, 3120000, 3480000, 3600000, 4440000, 5880000, 6120000,
7680000, 8400000, 8520000, 8640000, 8760000, 8880000, 9000000,
9120000, 10320000, 11280000, 12240000, 12360000, 12840000, 13080000,
14760000, 17520000, 17880000, 18120000, 18240000, 18480000, 18600000,
18720000, 19200000, 19320000, 20640000, 21000000, 21120000, 21840000,
22560000, 22680000, 24360000, 24600000, 24720000, 25080000, 25200000,
25440000, 25560000, 25680000, 25920000, 26160000, 26280000, 27000000,
27360000, 27480000, 27840000, 27960000, 28320000, 28440000, 28560000,
28680000, 29160000, 29280000, 29520000, 29760000, 29880000, 30000000,
30120000, 30360000, 30840000, 31200000, 31680000, 32760000, 33000000,
33360000, 33480000, 33600000, 33720000, 33840000, 34080000, 34200000,
34320000, 34440000, 34920000, 35040000, 35160000, 35400000, 35520000,
35640000, 35760000, 35880000, 36000000, 36120000, 36480000, 36720000,
36840000, 37440000, 37680000, 37800000), Means = c(45.1721105399911,
58.3236234466928, 10.701781072969, 81.1844097193854, 15.9764258576336,
72.9857717254786, 100.909692015799, 42.3842652589944, 48.5758167032384,
60.5307788344342, 9.72605226749078, 30.952302909114, 17.860141968134,
30.8530526895484, 20.4628162381967, 116.623581135536, 38.6678878887186,
78.9150157908195, 247.360337239763, 24.8838914877946, 23.429988222356,
53.2615600034024, 52.3424770503346, 170.222454449925, 50.5781138394727,
68.3087962976007, 89.4230029840393, 330.313625666045, 5.03584032143116,
89.2643864875047, 27.8653665885641, 201.299758574135, -5.42494623204948,
46.35601686698, 5.79103997302425, 112.341455197127, -4.28592603543802,
7.41453012965141, 54.7629963052909, 23.3995967033728, 38.50598295151,
51.1117491264575, 9.70064959823299, 145.915122377063, -1.93394721482472,
223.668891284723, 0.967813870514552, 3.98951268889225, 103.991761780532,
25.360339056567, 110.629872488342, 98.3711372064266, 4.29902758331359,
-6.49705043591403, 119.885301893303, 11.7856758287972, 2.14257993846943,
0.895276964913781, -4.13978377824383, 32.8265982947408, 102.894448568246,
16.4150366530933, 3.50639248897849, 96.4740592727108, 163.538533768379,
11.7417544456533, 271.336168593183, 21.9737935918722, 69.3505139183734,
39.0812235546367, -0.0979741416490998, 11.2593492499262, 1.09352485411191,
125.197079877443, 3.72187246405846, 60.0443035930762, 64.269810330157,
16.8509153029321, -1.53165469412626, 17.8174419767041, 12.4924416240186,
77.1154197241883, 50.0459666078323, 44.1948097160243, 7.87958496186204,
24.2661434245405, 36.080204093108, 57.8551517801946, 130.247092097128,
56.2802152403655, 24.1732000185415, 0.805669460114936, 20.805136831573,
89.3895887677943, 12.0889852368913, 189.261728063453, 18.3254402417783,
0.914727515857528, 26.4441526771417, 60.3908804957335)), .Names = c("chr",
"leftPos", "Means"), row.names = c(NA, 100L), class = "data.frame")
The code I am using for one of the plots (facet_wrap comes later)
UL1=400
LL1=0
Median1=200
ggplot(Zoutliers1,aes(x = leftPos,
y = as.numeric(Means),
group = chr,
xend = leftPos,
yend=0))+
#geom_bar(stat="identity",fill = "red", size = 1, colour = "red")+
geom_line()+
#geom_segment(linetype= 1, colour = "#919191")+
#ggtitle(TBBName)+
ylim(-100,480)+
facet_grid(.~chr, space="free_x", scales="free_x")+
geom_hline(yintercept = UL1,size=0.5)+
geom_hline(yintercept = Median1,size=0.5,colour='orange')+
geom_hline(yintercept = LL1,size=0.5)+
theme(panel.margin = unit(0.1, "lines"))+
theme(axis.text.x = element_blank())+
theme(panel.border = element_rect(fill=NA,color="darkred", size=0.5,
linetype="dashed"))+
theme(axis.title = element_blank())

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