-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathRead Me (plotParameter).txt
executable file
·129 lines (94 loc) · 7.73 KB
/
Read Me (plotParameter).txt
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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
Plot Parameters:
---------------------------
Coding 4in1 plot indices.
C1 C2
R1 11 12
R2 21 22
** stands for plot indices, 11, 12, 21 or 22.
-----------------------------------------------------------------------------------------------------------------------------------------
ui.R id Input/Output Description
-----------------------------------------------------------------------------------------------------------------------------------------
showPlots : TRUE/FALSE Shows 4in1 (2x2) CutOff plots.
cutoffPlotsOpts : TRUE/FALSE Activates extra plot options.
subGrps : Selectize Graph options to be modified (x-axis, y-axis, legend, other)
font.family : Selectize Font family to be used in figures (Times, Courier, Mono, Symbol)
selectedGraph : Character vector Tracks the selected plot to be modified (11, 12, 21 or 22)
main** : Character Graph title
font.main** : Selectize Graph title font (Regular, Italic, Bold, Bold Italic)
cex.main** : Numeric Size of graph title (between 0.1 and 5 in steps of 0.1)
col.main** : Character Title color
ROCcol11 : Character Color for ROC line. (Specific to plot 11. Any color from R color palette)
ROClty11 : Selectize ROC curve line type (One of line types from R whic is coded with numbers, 1:6)
specCol : Character Specificity line color (specific to figure 12)
sensCol : Character Sensitivity line color (specific to figure 12)
specType : Selectize Specificity line type (specific to figure 12)
senstype : Selectize Sensitivity line type (specific to figure 12)
lineColD : Character Line color for Diseased distribution (specific to figure 21)
lineColH : Character Line color for Healthy distribution (specific to figure 21)
lineTypeD : Selectize Line type for Diseased distribution (specific to figure 21)
lineTypeH : Selectize Line type for Healthy distribution (specific to figure 21)
xlab** : Character Label for x-axis.
xfont.lab** : Selectize Label font for x-axis (Regular, Italic, Bold, Bold Italic)
xcol.lab** : Character Color for x-axis label
xcex.lab** : Numeric Size of x-axis label (between 0.1 and 5 in steps of 0.1)
xcol.axis** : Character Color for x-axis annotations
xcex.axis** : Numeric Size of x-axis annotations (between 0.1 and 5 in steps of 0.1)
xcol** : Character Color for x-axis
xcol.ticks** : Character Tickmarks' color for x-axis
ylab** : Character Label for y-axis
yfont.lab** : Seleztize Label font for y-axis (Regular, Italic, Bold, Bold Italic)
ycol.lab** : Character Color for y-axis label
ycex.lab** : Numeric Size of y-axis label (between 0.1 and 5 in steps of 0.1)
ycol.axis** : Character Color for y-axis annotations
ycex.axis** : Numeric Size of y-axis annotations (between 0.1 and 5 in steps of 0.1)
ycol** : Character Color for y-axis
ycol.ticks** : Character Tickmarks' color for y-axis
pchSize : Numeric Size of the points
colPoints : Character vector Point colors for Healthy and Diseased points (specific to figure 22)
pchPoints : Numeric Point type (Pre-defined number within 0-25. See R pch styles)
pchFill : Character vector Fill color for points with pchPoints within 21-25
xlabels22 : Character vector x-axis labels for figure 22.
jitterAmount : Numeric Amount of jittering for figure 22.
legendPos** : Selectize Position of legend (for figure 12 and 21 - Top right(tr), Top left(tl), Bottom right(br), Bottom left(bl))
legendXpos** : Numeric x position of legend
legendYpos** : Numeric y position of legend
legendNames** : Character vector Legend labels
cex.legend** : Numeric Size of legend labels and title
legendTitle** : Character Legend title
font.legendTitle** : Selectize Font for legend title
col.legendTitle** : Character Color for legend title
-----------------------------------------------------------------------------------------------------------------------------------------
## Optimal Cutpoints control parameters.
-----------------------------------------------------------------------------------------------------------------------------------------
ui.R id Input/Output Description
-----------------------------------------------------------------------------------------------------------------------------------------
CFP_Youden : Numeric Cost of a False Positive (if method is "Youden")
CFN_Youden : Numeric Cost of a False Negative (if method is "Youden")
generalized_Youden : TRUE/FALSE Generalized Youden index should be calculated? (Default is FALSE)
costs_benefits_Youden : TRUE/FALSE Cost-benefit based Youden incex should be calculated? (Default is FALSE)
costs_ratio : Numeric Cost ratio to be used with the method "CB"
CFP_MCT : Numeric Cost of a False Positive (if method is "MCT")
CFN_MCT : Numeric Cost of a False Negative (if method is "MCT")
valueSp_MVSp : Numeric Value of specificity (if method is "MinValueSp")
valueSe_MVSe : Numeric Value of sensitivity (if method is "MinValueSe")
valueSe_VSe : Numeric Value of sensitivity (if method is "ValueSe")
valueSp_VSp : Numeric Value of specificity (if method is "ValueSp")
valueSp_MVSpSe : Numeric Value of specificity (if method is "MinValueSpSe")
valueSe_MVSpSe : Numeric Value of sensitivity (if method is "MinValueSpSe")
maxSp_MVSpSe : TRUE/FALSE Should specificity be maximized if multiple optimal cutpoints are found? (Default is TRUE)
CFP_MK : Numeric Cost of a False Positive (if method is "MaxKappa")
CFN_MK : Numeric Cost of a False Negative (if method is "MaxKappa")
weighted_Kappa : TRUE/FALSE Should weighted kappa be computed? (Default is FALSE)
costs_benefits_Efficiency : TRUE/FALSE Cost-benefit based optimal cut off (if method is "MaxEfficiency")
standard_deviation_accuracy : TRUE/FALSE Standard deviation associated with accuracy at optimal cut points (if method is "MaxEfficiency")
valueNPV_MVNPV : Numeric Value of NPV (if method is "MinValueNPV")
valuePPV_MVPPV : Numeric Value of PPV (if method is "MinValuePPV")
valueNPV_VNPV : Numeric Value of NPV (if method is "valueNPV")
valuePPV_VPPV : Numeric Value of NPV (if method is "valuePPV")
valueNPV_MVNPVPPV : Numeric Value of NPV (if method is "MinValueNPVPPV")
valuePPV_MVNPVPPV : Numeric Value of PPV (if method is "MinValueNPVPPV")
maxNPV_MVNPVPPV : TRUE/FALSE Should NVP be maximized if multiple optimal cut points are found? (Default is TRUE)
valueDLR_Negative : Numeric Value of Negative Diagnostic Likelihood Ratio.
valueDLR_Positive : Numeric Value of Positive Diagnostic Likelihood Ratio.
adjusted_pvalue : Selectize Method for adjusting p-value (if method is "MinPvalue")
-----------------------------------------------------------------------------------------------------------------------------------------