marrow | A boilerplate for backbone.js | Frontend Framework library
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kandi X-RAY | marrow Summary
Marrow is a boilerplate for backbone.js.
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QUESTION
This was my earlier question where it was solved using multiple distribution.
I want to plot the continuous variable like age or tumor mutation burden as shown in first figure with a range like a window such 20-30 age group or some mutational burden range
The frequencies are calculated for all the variables of the metadata, but when plotting the age is not mapped to the final plot as show in the second plot.
Does the age need to be converted into other class before plotting?
...ANSWER
Answered 2022-Mar-14 at 09:14Rename Diagnosis-Age
and use cut
to convert to a factor. Add labels as required for appearance of age groups in legend.
Note I have swapped name
and perc
in the call to aes
to avoid the call to coord_flip
.
QUESTION
ANSWER
Answered 2022-Mar-02 at 12:15library(tidyverse)
library(ggnewscale)
plot_meta <- structure(list(
patient = structure(c(
36L, 33L, 122L, 95L, 66L,
49L
), .Label = c(
"TCGA-AB-2805", "TCGA-AB-2806", "TCGA-AB-2808",
"TCGA-AB-2810", "TCGA-AB-2811", "TCGA-AB-2812", "TCGA-AB-2813",
"TCGA-AB-2814", "TCGA-AB-2815", "TCGA-AB-2817", "TCGA-AB-2818",
"TCGA-AB-2819", "TCGA-AB-2820", "TCGA-AB-2821", "TCGA-AB-2822",
"TCGA-AB-2823", "TCGA-AB-2825", "TCGA-AB-2826", "TCGA-AB-2828",
"TCGA-AB-2830", "TCGA-AB-2834", "TCGA-AB-2835", "TCGA-AB-2836",
"TCGA-AB-2839", "TCGA-AB-2840", "TCGA-AB-2841", "TCGA-AB-2842",
"TCGA-AB-2843", "TCGA-AB-2844", "TCGA-AB-2845", "TCGA-AB-2846",
"TCGA-AB-2847", "TCGA-AB-2849", "TCGA-AB-2851", "TCGA-AB-2853",
"TCGA-AB-2856", "TCGA-AB-2857", "TCGA-AB-2858", "TCGA-AB-2859",
"TCGA-AB-2861", "TCGA-AB-2862", "TCGA-AB-2863", "TCGA-AB-2865",
"TCGA-AB-2866", "TCGA-AB-2867", "TCGA-AB-2869", "TCGA-AB-2870",
"TCGA-AB-2871", "TCGA-AB-2872", "TCGA-AB-2873", "TCGA-AB-2874",
"TCGA-AB-2875", "TCGA-AB-2876", "TCGA-AB-2877", "TCGA-AB-2878",
"TCGA-AB-2880", "TCGA-AB-2881", "TCGA-AB-2882", "TCGA-AB-2883",
"TCGA-AB-2884", "TCGA-AB-2885", "TCGA-AB-2886", "TCGA-AB-2888",
"TCGA-AB-2889", "TCGA-AB-2890", "TCGA-AB-2891", "TCGA-AB-2892",
"TCGA-AB-2893", "TCGA-AB-2894", "TCGA-AB-2895", "TCGA-AB-2896",
"TCGA-AB-2897", "TCGA-AB-2898", "TCGA-AB-2899", "TCGA-AB-2900",
"TCGA-AB-2901", "TCGA-AB-2908", "TCGA-AB-2910", "TCGA-AB-2911",
"TCGA-AB-2912", "TCGA-AB-2913", "TCGA-AB-2914", "TCGA-AB-2915",
"TCGA-AB-2916", "TCGA-AB-2917", "TCGA-AB-2918", "TCGA-AB-2919",
"TCGA-AB-2920", "TCGA-AB-2921", "TCGA-AB-2924", "TCGA-AB-2925",
"TCGA-AB-2927", "TCGA-AB-2928", "TCGA-AB-2929", "TCGA-AB-2930",
"TCGA-AB-2931", "TCGA-AB-2932", "TCGA-AB-2933", "TCGA-AB-2934",
"TCGA-AB-2935", "TCGA-AB-2936", "TCGA-AB-2937", "TCGA-AB-2938",
"TCGA-AB-2939", "TCGA-AB-2940", "TCGA-AB-2941", "TCGA-AB-2942",
"TCGA-AB-2943", "TCGA-AB-2944", "TCGA-AB-2946", "TCGA-AB-2948",
"TCGA-AB-2949", "TCGA-AB-2950", "TCGA-AB-2952", "TCGA-AB-2955",
"TCGA-AB-2956", "TCGA-AB-2959", "TCGA-AB-2963", "TCGA-AB-2965",
"TCGA-AB-2966", "TCGA-AB-2970", "TCGA-AB-2971", "TCGA-AB-2973",
"TCGA-AB-2975", "TCGA-AB-2976", "TCGA-AB-2977", "TCGA-AB-2979",
"TCGA-AB-2980", "TCGA-AB-2981", "TCGA-AB-2982", "TCGA-AB-2983",
"TCGA-AB-2984", "TCGA-AB-2986", "TCGA-AB-2987", "TCGA-AB-2988",
"TCGA-AB-2990", "TCGA-AB-2991", "TCGA-AB-2992", "TCGA-AB-2994",
"TCGA-AB-2995", "TCGA-AB-2996", "TCGA-AB-2998", "TCGA-AB-2999",
"TCGA-AB-3000", "TCGA-AB-3001", "TCGA-AB-3002", "TCGA-AB-3007",
"TCGA-AB-3008", "TCGA-AB-3009", "TCGA-AB-3011", "TCGA-AB-3012"
), class = "factor"), Sex = structure(c(2L, 2L, 1L, 1L, 2L, 2L), .Label = c("Female", "Male"), class = "factor"), FAB = structure(c(
5L,
1L, 5L, 3L, 2L, 4L
), .Label = c(
"M0", "M1", "M2", "M3", "M4",
"M5", "M6", "M7", "nc"
), class = "factor"), `Diagnosis-Age` = c(
63L,
39L, 76L, 62L, 42L, 42L
), `Bone-Marrow-Blast-Percentage` = c(
82L,
83L, 91L, 72L, 68L, 88L
), Cytogenetics = structure(c(
75L, 93L,
51L, 27L, 21L, 57L
), .Label = c(
"37~49,XY,+Y,der(1)add(1)(p13)del(1)(q21q25),-5,der(7)inv(7)(p15q11.2)?inv(7)(q22q32),+17,add(17)(p13),+21,+mar[cp20]",
"39~47,XX,del(5)(q13q33),-7,der(8)t(8;?8;8)(p23;?p11.2p23;q11.2),der(14)t(1;14)(p12;p11.2)der(1)t(7;16)(p15;q22),+2mar[cp19]",
"41~44,X,?i(X)(p10),-7,der(12)t(8;12)(q11.2;p11.2),-8 [cp11]/46,XX[8[",
"42,XY,-5,-7,add(12)(p13),t(14;15)(q10;q10),der(17)t(5;17)(p13;p11.2),-18[6]/40,idem,-11,-add(12)(p13),der(12)t(?;12)(?;p13),-19[6]/41,idem,-der(17)[3]/41,idem,-der(17),+mar1,+mar[3]/41,idem,der(1)der(1)(p12)add(1)(p12),+der(1)(q21)add(1)(q21),-3,-8[2]",
"43,XY-3,del(5)(q12q33),-7,der(10)t(10;11)(q26;q13),-12,-18,+2mar[20]",
"44-45,X,-Y,-5,add(16)(q22),-17,-18,iso(21),+mars[cp5]/82-84,XX,-Y,-3,-4,-11,-12,-19,-21,+21[cp5}",
"44~46,XX,del(11)(q23),der(19)?t(11;19)(q23;p13.1)[cp11]/44~45,XX,-19[cp4]/46,XX [5]",
"44~47,XX,t(1;15)(q32;q26)[14],del(5)(q13q33)[19],-7[20],+8[7],del(12)(p11.2p11.2)[15],del(17)(q21)[8],der(22)t(1;22)(p13;p11.2)[20],+mar[13][cp20]",
"44~47,XY,del(5)(q22q35)[20],-7[14],-8[6],der(12)t(10;12)(p11.2q21)[2],add(14)(p12)[11],-17[13],der(17)t(10;17)(q11.2;p13)[14],-18[7],add(18)(p11.2)[7],-21[10],i(21)(q10)[4],-22[4],+mar[10],+mar1x2[6][cp20]",
"45,X,-X,t(8;21)(q22;q22)[20]", "45,X,-Y, t(8;7;21)(q22;p15;q22[22]/46,XY[3]",
"45,X,-Y,t(8;21)(q22;q22)[13]/45,idem,del(9)(q22;q32)[7]", "45,X,-Y,t(8;21)(q22;q22)[19]/46,XY[1]",
"45,X,-Y[3]/46,XY [17]", "45,XX-7[5]-only 5 metaphases", "45,XX,-7,t(9;11)(p22;q23)[19]/46,XX[1]",
"45,XX,-7[12]/46,XX[8]", "45,XX,-7[20]", "45,XY,-7, t(9;22)(q34;q11.20) [19]/46,XY[1]",
"45,XY,-7[20]", "45,XY,der(7)(t:7;12)(p11.1;p11.2),-12,-13,+mar[19]/46,XY[1]",
"45~46,XY,add(X)(q22)[7],Y[4],der(5)t(5;17)(q13;21)[18],-7[18],+8[17],del(12)(q23)[16],-17[18],add(18)(p11.2)[14][cp18]",
"46, XX[14]", "46, XX[15]", "46, XX[16]", "46, XX[19]", "46, XX[20]",
"46, XY[15]", "46, XY[20]", "46,XX,1~50dmin[12]/46,idem,der(6)t(6;?)(q22;?)[2]/46,XX[6]",
"46,XX,9qh+[20]", "46,XX,del(3)(q23q26.2),der(7)t(1:7)(q32;q32),del(10)(q22q25),t(13;16)(q34;p11.2)dup(21)(q22)[cp20]",
"46,XX,del(5)(q11.2q33)[1]/48~52,idem,+1,+?del(5)(q15q33),+11,+11,?t(12;22)(p13;q12),-13,-17,+i(22)(q10),+i(22)(q10),+mar[cp19]",
"46,XX,del(5)(q22q33)[4]/46,XX[16]", "46,XX,i(17)(q10)[1]/45,sl-7[2]/48,sl,+13,+19[3]/46,XX[15]",
"46,XX,inv(16)(p13q22)[15]/46,XX[2]", "46,XX,inv(16)(p13q22)[19]/46,XX[1]",
"46,XX,inv(16)(p13q22)[20]", "46,XX,inv(16)(p13q22)[5]/46,idem,t(3;3)(p13;q?28)[5]/46,XX[6]",
"46,XX,t(15;17)(q22;q21.1)[19]/47,idem,+8 [1]", "46,XX,t(15;17)(q22;q21),t(16;19)(p13.3;p13.1)[17]/46,XX[3]",
"46,XX,t(15;17)(q22;q21)[11]/46,XX[9]", "46,XX,t(15;17)(q22;q21)[12]/46,XX[8]",
"46,XX,t(15;17)(q22;q21)[20]", "46,XX,t(8;21)(q22;q22)[17]/46,XX[3]",
"46,XX,t(8;21)(q22;q22)[20]", "46,XX,t(8;21)[15]/46,idem,del(9)(q12q22)[5]",
"46,XX[15]", "46,XX[18]", "46,XX[19]/46,XX,add(7)(p?22)[1]",
"46,XX[20]", "46,XX+13,21[cp17]/46,XX[3]", "46,XY,9qh+[19]",
"46,XY,del(11)(p12)[2]/46,XY[18]", "46,XY,del(20)(q11.2)[23]/92,XXYY,del(20)(q11.2)x2[2]/46,XY[3]",
"46,XY,del(7)(q21q36)[18]/46,XY[2]", "46,XY,del(9)(q13:q22),t(11:21)(p13;q22),t(15;17)(q22;q210[20]",
"46,XY,i(17)(q10)[15]/47,XY,idem+13[3]/46,XY[2]", "46,XY,inv(16)(p13;q22)[20]",
"46,XY,inv(16)(p13q22)[17]/46,XY[3]", "46,XY,inv(16)(p13q22)[9]/46,XY[10]",
"46,XY,t(11;19)(q23;p13)[17]/46,XY,t(11;19)(q23;p13),inv(12)(p12p13)[3]",
"46,XY,t(11;19)(q23;p13)[20]", "46,XY,t(15;17)(q22;q21)[19]/46,XY[1]",
"46,XY,t(15;17)(q22;q21)[20]", "46,XY,t(15;17)(q22:q21)[11]/46,XY[9]",
"46,XY,t(2;4)(q34;q21)inv(16)(p13q22) [20]", "46,XY,t(6;11)(q27;q23)[15]",
"46,XY,t(9;11)(p22;q23)[7]/47,XY,t(9;11)(p22;q23)[7]/46,XY[4]",
"46,XY,t(9;22)(q34;q11.2)[13]/34~37,idem,-3,del(4),-4,-5,-7,-9,-10,t?(11;12),-12,-14,-14,-16,-17,-22[cp6]/46,XY[1]",
"46,XY,t(9;22)(q34;q11.2[4]/50,idem,+8,+10,+21,+der(22)(t(9;22)(q34;q11.2)[16]",
"46,XY[13]", "46,XY[15]", "46,XY[19]", "46,XY[20]", "46,XY[30]",
"46~49,XY,del(3)(p14),del(5)(p11.2q33),del(17)(q21q21),add(21)(p11.2),+22,mar[cp20]",
"47,XX,+der(5)t(2;5)(p11.2;q11.2)?,t(8;16)(p11.2;p13.3)[19]",
"47,XX,i(11)(q10)[18]/46,XX [2]", "47,XX,t(15;17)(q22:q21)+mar[20]",
"47,XX+11 [20]", "47,XX+8 [20]", "47,XXY [17]", "47,XY,+13[5]/46,XY[15]",
"47,XY,+21 [6]/46,XY[13]", "47,XY,+21[11]/48,XY,+3,+21[8]", "47,XY,+22[10]/47,XY,+8[7]/45,XY,del(3)(p21),del(4)(p12p15),-7,?dup(7)(q11.2q36)[3]",
"47,XY,+8 [10]/46,XY [10]", "47,XY,+8 [19]", "47,XY,+8 [20]",
"47,XY,+8[15]/46,+8,-17[3]", "47,XY,+9[10]/46,XY[10]", "47,XY,del(5)(q22q33),t(10;11)(p13~p15;q22~23),i(17)(q10)[3]/46,XY[17]",
"47,XY,del(7)(q22),+8,t(15;17)(q22;q21)[18]/46,XY,del(7)(q22),t(15;17)(q22;q21)[2]",
"47,XY+8 [15]/48,XY+8+8[4]/46,XY[1]", "48,XY,+8,+8[16]/46,XY[4]",
"52~54,XY,+2,+4,+6,+8,del(11)(q23),+19,+19,+21[17]/46,XY[3]",
"53~56,XY,+1,del(2)(q33q34),+8,+10,+11x2,+13x1-2,+14,del(17)(p11.2),+19,add(21)(q22),+22[cp20]",
"incomplete-46,XY,del(12)(p11.20[2]/46,XY[3]", "N.D.", "ND",
"Outside hospital with inv(16)"
), class = "factor"), `Cytogenetic-Code--Other-` = structure(c(
8L,
3L, 8L, 8L, 3L, 9L
), .Label = c(
"BCR-ABL1", "CBFB-MYH11", "Complex Cytogenetics",
"Intermediate Risk Cytogenetic Abnormality", "MLL translocation, poor risk",
"MLL translocation, t(9;11)", "N.D.", "Normal Karyotype", "PML-RARA",
"Poor Risk Cytogenetic Abnormality", "RUNX1-RUNX1T1"
), class = "factor"),
Induction = structure(c(11L, 4L, 1L, 8L, 4L, 9L), .Label = c(
"7+3",
"7+3, dauna", "7+3, IT", "7+3+3", "7+3+3, gleevec", "7+3+3, then 5+2+2",
"7+3+3+PSC", "7+3+AMD", "7+3+ATRA", "7+3+dauno", "7+3+Genasense",
"7+3+study drug", "7+4+ATRA", "Azacitidine", "CLAM", "Cytarabine only",
"Decitabine", "Decitabine then 7+3", "Hydrea & Idarubicin",
"Hydrea, ATRA started", "hydrea, didn't get add'l chemo",
"LBH/Decitabine", "low dose Ara C", "no treatment", "Revlimid",
"Revlmd then Decitbne,7+3,5+2"
), class = "factor")
), row.names = c(
NA,
6L
), class = "data.frame")
df <-
plot_meta %>%
mutate(across(everything(), as.character)) %>%
pivot_longer(everything()) %>%
count(name, value) %>%
group_by(name) %>%
mutate(perc = n / sum(n) * 100)
df
#> # A tibble: 38 × 4
#> # Groups: name [8]
#> name value n perc
#>
#> 1 Bone-Marrow-Blast-Percentage 68 1 16.7
#> 2 Bone-Marrow-Blast-Percentage 72 1 16.7
#> 3 Bone-Marrow-Blast-Percentage 82 1 16.7
#> 4 Bone-Marrow-Blast-Percentage 83 1 16.7
#> 5 Bone-Marrow-Blast-Percentage 88 1 16.7
#> 6 Bone-Marrow-Blast-Percentage 91 1 16.7
#> 7 Cytogenetic-Code--Other- Complex Cytogenetics 2 33.3
#> 8 Cytogenetic-Code--Other- Normal Karyotype 3 50
#> 9 Cytogenetic-Code--Other- PML-RARA 1 16.7
#> 10 Cytogenetics 45,XY,der(7)(t:7;12)(p11.1;p11.2),-… 1 16.7
#> # … with 28 more rows
df %>%
ggplot(aes(name, perc)) +
geom_col(data = ~ filter(.x, name == "FAB") %>% rename(FAB = value), mapping = aes(fill = FAB)) +
new_scale_fill() +
geom_col(data = ~ filter(.x, name == "Sex") %>% rename(Sex = value), mapping = aes(fill = Sex)) +
new_scale_fill() +
geom_col(data = ~ filter(.x, name == "Induction") %>% rename(Induction = value), mapping = aes(fill = Induction)) +
coord_flip()
QUESTION
I have a list of brain metastasis MRIs that I want to use for training and testing purposes. These images are all similar but the original tumor sites differs. See the following example:
From Lungs:
- "Image01.1"
- "Image01.2"
- "Image01.3"
- "Image01.4"
From Breasts:
- "Image02.1"
- "Image02.2"
- "Image02.3"
- "Image02.4"
- "Image02.5"
From Skin:
- "Image03.1"
- "Image03.2"
From Lung Tissue:
- "Image04.1"
- "Image04.2"
- "Image04.3"
From Bone Marrow:
- "Image05.1"
- "Image05.2"
I want the testing and validation set to contain the same amount of images without losing a similar composition (both lists containing the same amount of each subtype).
For this purpose can I create lists for each subtype and then randomly split those 50/50. Followed by adding all these lists together?
...ANSWER
Answered 2021-Sep-12 at 22:53If you want to get specific rows from a pandas DataFrame that meet certain criteria, you can filter. In your case, something like:
QUESTION
I have a MySQL table with some addresses on it. I would like to find the addresses that contain double letters between the 5th and 11th position. There is a test table with some data for reference.
...ANSWER
Answered 2021-Aug-18 at 19:39Use SUBSTR()
to get the substring between 5th and 11th position.
QUESTION
I'm a complete beginner with coding and decided to try out android studios for fun without having formal training or lessons for the basics so I'm sorry if this seems like a dumb problem but whenever I try to run my code it just comes off as blank? Any idea how to solve this?
Here's a screenshot of what comes up
...ANSWER
Answered 2021-Jul-09 at 18:33Did you clean and rebuild your project or Invalid caches/restart from IDE?You will find it in under File menu.
It seems like your code is fine , so I decided to run in IDE its compiling and running perfectly .
Firebase console-
So you can do some checks in your side - 1.
QUESTION
Here is my sample data and code. I wanna add two wards in specific location just as the picture shows below.
...ANSWER
Answered 2021-Apr-11 at 12:38I found a better way to add text outside plot region.
just like this:
QUESTION
Here is my code and sample data:
I wanna all of the bars have the same width. Now it's not so.
...ANSWER
Answered 2021-Apr-10 at 11:09Here is now the solution: @teunbrand: Sorry for this but I really got nervous after you commented my first answer. I just messed up something. After checking facet_nested
I come to this solution:
Just add space = "free_x"
to facet_nested
QUESTION
Here is my sample data and code:
Now I wanna adjust the blank region to different colors. And I used the ggh4x package () and its vital function: facet_nested(.~Organ+Disease, scales="free",switch = "x",nest_line = TRUE)
...ANSWER
Answered 2021-Apr-10 at 10:00There is no nice function to do this, but you can manually change the colours of the strips if you want to get your hands dirty with some gtable
QUESTION
I have a table with two columns, one column (AffiliationCountry) shows the countries and the other column (ArtSubareaKeyword) shows the subject areas in related countries with comma-separated values.
I want to extract the subject area which is repeating for a country the same country one or more times and save it in a new column with the name "MostPopularSubjectArea".
Table with values:
As you can see in the table that a country is repeating and its values are also repeating.
AffiliationCountry ArtSubareaKeyword1 ArtSubareaKeyword1 ArtSubareaKeyword1 Spain Cell membranes Cell staining Coimmunoprecipitation Kazakhstan Factor analysis Human performance Immunofluorescence Japan Bone marrow Diagnostic medicine Genetic loci Kazakhstan Drug research Factor analysis Human performanceResults that are required:
I want a SQL query that can store for that country a new column that stores the common subjects area which is occurring more.
AffiliationCountry MostPopularSubjectArea Kazakhstan Human performance ...ANSWER
Answered 2021-Apr-03 at 08:49As per the table, you can select the pair of columns, union them and find the count using group by:
QUESTION
I am a beginner to Java and I have a health insurance program, which returns a total quote based on if the customer has any health conditions already present or not. Each health condition increases the total amount by a different %, and there can be more than one health condition present, in which case the total will be increased according to the order of the if statements. For example, the customer may have "Bone marrow", in which case the total is multiplied by 20%, or they may have "Bone marrow" and "Cancer" in which case the total is increased by 20% and then 25% in that order.
I have this written in multiple independent if statements because unlike with an if else statement, there can be more than one health condition present. Is there a way I can write this in a way that's more elegant than just a long list of if statements?
...ANSWER
Answered 2021-Mar-17 at 21:17It seems that switch
statement is more appropriate in this case:
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